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Dear all,
I'm trying to phase SAD data with OASIS at 3.0 A resolution. It seems
that there is a problem with the last shell during the wilson
calculation. I pasted the output below.
I tried several resolution limits but nothing changes.
Then Oasis abandons with error messages concerning format.
Does anybody have any hints ?
Thank you very much in advance,
Cheers,
Vanessa.
****** OASIS ******
Version 1.2.2, 09 Jan 2003
A program for phasing OAS (One-wavelength Anomalous Scattering)
or SIR (Single Isomorphous Replacement) data
Authors: Q.Hao (1,2), Y.X.Gu, C.D.Zheng & H.F.Fan (2)
(1) Cornell University, USA
(2) Institute of Physics, Chinese Academy of Sciences
Email: [EMAIL PROTECTED] or [EMAIL PROTECTED]
FORMATTED SCRATCH file opened on unit 10
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: KEYWORD, Filename: /tmp/vanessa/oasis_keyword.31289
<!--SUMMARY_END--></FONT></B>
FORMATTED SCRATCH file opened on unit 1
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: SIGNDT, Filename: /tmp/vanessa/oasis_signdt.31289
<!--SUMMARY_END--></FONT></B>
FORMATTED SCRATCH file opened on unit 9
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: PROTDT, Filename: /tmp/vanessa/oasis_protdt.31289
<!--SUMMARY_END--></FONT></B>
UNFORMATTED SCRATCH file opened on unit 8
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: SCRA8, Filename: /tmp/vanessa/oasis_scra8.31289
<!--SUMMARY_END--></FONT></B>
PROGRAM FOR PRELIMINARY PROCESSING OF INPUT DATA VERSION
1999
TITLE OAS phasing using Gd derivative
30/10/06 18:04:20
UNIT CELL: A = 110.755 B = 137.318 C = 143.419
ALPHA = 86.87 BETA = 74.00 GAMMA = 86.01
SYMMETRY CLASS: TRICLINIC
SPACE GROUP: P 1
H EQUIVALENT POSITIONS:
1. X Y Z
HIGH RESOLUTION LIMIT = 3.000 ANGSTROM
UNIT CELL CONTENTS:
ATOM NUMBER IN CELL ATOMIC NUMBER
C 37312 6
N 8960 7
O 10496 8
S 224 16
GD 8 64
SCATTERING FACTOR CONSTANTS:
F=AA*EXP(-A*RHO)+BB*EXP(-B*RHO)+CC*EXP(-C*RHO)+DD*EXP(-D*RHO)+E
AA A BB B CC C DD D
E
C 2.310 20.844 1.020 10.208 1.589 0.569 0.865 51.651
0.216
N 12.213 0.006 3.132 9.893 2.013 28.997 1.166 0.583
-11.529
O 3.049 13.277 2.287 5.701 1.546 0.324 0.867 32.909
0.251
S 6.905 1.468 5.203 22.215 1.438 0.254 1.586 56.172
0.867
GD 25.071 2.253 19.080 0.182 13.852 12.933 3.545 101.398
2.420
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: toto.mtz
* Title:
XDS to MTZ
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions,
wavelength:
1 unknown
unknown
unknown161006
110.7550 137.3180 143.4190 86.8680 73.3950 86.0140
0.00000
* Number of Columns = 9
* Number of Reflections = 156651
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FP SIGFP DANO SIGDANO ISYM FreeRflag
* Column Types :
H H H F Q D Q Y I
* Associated datasets :
0 0 0 1 1 1 1 1 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
110.7550 137.3180 143.4190 86.8680 73.3950 86.0140
* Resolution Range :
0.00051 0.11111 ( 44.455 - 3.000 A )
* Sort Order :
1 2 3 0 0
* Space group = 'P 1' (number 1)
NUMBER OF ATOMS IN ASYMMETRIC UNIT = 57000.00
TOTAL NUMBER OF REFLEXION (IN DATA-FILE) =156651
MAXIMUM (SIN(THETA)/LAMBDA)**2 = 0.0280
NUMBER OF POINTS ON WILSON PLOT = 30
EXP(-2*B*RHO)*E**2
RANGE (SIN/LAM)**2 NUMBER MEAN RHO MEAN I MEAN DEBYE
WILSON
1 0.0000 -0.0019 2743 0.0011 1979357.8 0.8053 -0.2165
-0.2165
2 0.0009 -0.0028 4131 0.0019 2208765.8 0.9195 -0.0839
-0.0839
3 0.0019 -0.0037 5072 0.0028 2131416.0 0.9079 -0.0966
-0.0966
4 0.0028 -0.0047 5867 0.0038 1653068.2 0.7209 -0.3273
-0.3273
5 0.0037 -0.0056 6595 0.0047 1192173.1 0.5337 -0.6279
-0.6279
6 0.0047 -0.0065 7188 0.0056 1013024.9 0.4658 -0.7640
-0.7640
7 0.0056 -0.0075 7750 0.0066 1001745.9 0.4725 -0.7497
-0.7497
8 0.0065 -0.0084 8324 0.0075 1040167.1 0.5029 -0.6874
-0.6874
9 0.0075 -0.0093 8781 0.0084 1245205.0 0.6174 -0.4822
-0.4822
10 0.0084 -0.0103 9225 0.0093 1471620.8 0.7464 -0.2925
-0.2925
11 0.0093 -0.0112 9695 0.0103 1628481.5 0.8458 -0.1674
-0.1674
12 0.0103 -0.0121 10161 0.0112 1843938.9 0.9803 -0.0199
-0.0199
13 0.0112 -0.0131 10545 0.0121 1865081.9 1.0131 0.0130
0.0130
14 0.0121 -0.0140 10851 0.0131 1807937.4 1.0049 0.0049
0.0049
15 0.0131 -0.0149 11225 0.0140 1816607.2 1.0321 0.0316
0.0316
16 0.0140 -0.0159 11656 0.0149 1666452.6 0.9671 -0.0335
-0.0335
17 0.0149 -0.0168 12005 0.0159 1564321.6 0.9288 -0.0738
-0.0738
18 0.0159 -0.0177 12351 0.0168 1496142.4 0.9071 -0.0975
-0.0975
19 0.0168 -0.0187 12681 0.0177 1351675.0 0.8372 -0.1777
-0.1777
20 0.0177 -0.0196 12868 0.0187 1256156.1 0.7945 -0.2300
-0.2300
21 0.0187 -0.0205 13243 0.0196 1179715.1 0.7619 -0.2720
-0.2720
22 0.0196 -0.0215 13610 0.0205 1078181.1 0.7104 -0.3420
-0.3420
23 0.0205 -0.0224 13759 0.0215 946716.9 0.6365 -0.4518
-0.4518
24 0.0215 -0.0233 14104 0.0224 845481.6 0.5800 -0.5448
-0.5448
25 0.0224 -0.0243 14476 0.0233 742565.2 0.5192 -0.6554
-0.6554
26 0.0233 -0.0252 14663 0.0243 671507.4 0.4792 -0.7356
-0.7356
27 0.0243 -0.0261 14878 0.0252 643153.8 0.4678 -0.7596
-0.7596
28 0.0252 -0.0271 15121 0.0261 581262.9 0.4308 -0.8422
-0.8422
29 0.0261 -0.0280 13203 0.0269 521457.0 0.3929 -0.9342
-0.9342
30 0.0271 -0.0280****** 0.0000 2.5 0.0000 -13.1874
-13.1874
NORMAL EQUATIONS
0.983E+02 * SLOPE + 0.519E+04 * INTERCEPT = -0.427E+04
0.519E+04 * SLOPE + 0.112E+10 * INTERCEPT = -0.148E+11
SLOPE=653.008 INTERCEPT=****** TEMPERATURE FACTOR(B)=-326.50
SCALE=*******
SQRT(SCALE)*F(OBS) = EXP(-B*RHO)*F(CAL)
***** NORMALIZATION BY LEAST SQUARES STRAIGHTLINE *****
AVERAGE E**2 ACCORDING TO APPROPRIATE INDEX GROUP BEFORE
RESCALING
PARITY GROUPS
ALL EEE OEE EOE OOE EEO OEO EOO
OOO
E**2 1.000 1.344 0.719 0.698 1.171 0.730 1.238 1.371
0.730
NUMBER 156651 19596 19547 19586 19599 19588 19572 19589
19574
TEMPERATURE AND SCALING FACTORS DERIVED BY THE PROGRAM
--- EXP{(-2*BT)*RHO}*FCAL**2=SCALE*FOBS**2 ---
GROUP 2*BT SCALE
ALL -653.0078 73.6818
FINAL STATISTICS
DISTRIBUTION OF E**2 WITH SIN(THETA)/LAMBDA
SIN/LAM0.0167 0.0335 0.0502 0.0669 0.0836 0.1004 0.1171 0.1338 0.1506
0.1673
E**2 ******31.116520.1503 6.4906 0.9004 0.1854 0.0361 0.0031 0.0001
0.0000
NUMBER 111 1145 3072 5972 9807 14627 20311 26906 34329
40371
AVERAGE VALUES
AVERAGE EXPERIMENTAL
THEORETICAL
ALL DATA HKL 0KL H0L HK0 ACENT CENT
H-CENT
MOD(E) 0.313 0.293 0.718 0.628 0.691 0.886 0.798
0.718
E**2 1.000 0.871 3.259 3.448 3.140 1.000 1.000
1.000
E**3 6.602 5.282 25.403 36.055 26.121 1.329 1.596
1.916
E**4 64.717 46.248264.219528.156321.137 2.000 3.000
4.500
E**5 841.205518.665********************* 3.323 6.383
12.260
E**6 *********************************** 6.000 15.000
37.500
HMOD(E**2-1) 1.763 1.645 3.785 4.045 3.689 0.736 0.968
1.145
(E**2-1)**2 63.731 45.514258.703522.263315.858 1.000 2.000
3.500
(E**2-1)**3 *********************************** 2.000 8.000
26.000
(MOD(E**2-1))**3 *********************************** 2.415 8.691
26.903
WEIGHTED SAMPLE SIZE156651 148825 2695 2559 2455
DISTRIBUTION OF E - NUMBER OF E'S .GT. LIMIT
E 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.5 1.6
NO. 15825 14236 12901 11904 11066 10296 9618 9000 8445 7949
E 1.7 1.8 1.9 2.0 2.1 2.2 2.3 2.4 2.5
NO. 7513 7052 6683 6303 5958 5639 5361 5065 4824
30/10/06 18:04:22
--- PREPARE COMPLETED ---
UNFORMATTED SCRATCH file opened on unit 8
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: SCRA8, Filename: /tmp/vanessa/oasis_scra8.31289
<!--SUMMARY_END--></FONT></B>
PROGRAM FOR PRELIMINARY PROCESSING OF INPUT DATA VERSION
1999
TITLE OAS phasing using Gd derivative
30/10/06 18:04:22
UNIT CELL: A = 110.755 B = 137.318 C = 143.419
ALPHA = 86.87 BETA = 74.00 GAMMA = 86.01
HIGH RESOLUTION LIMIT = 3.000 ANGSTROM
UNIT CELL CONTENTS:
ATOM NUMBER IN CELL ATOMIC NUMBER
GD 8 64
SCATTERING FACTOR CONSTANTS:
F=AA*EXP(-A*RHO)+BB*EXP(-B*RHO)+CC*EXP(-C*RHO)+DD*EXP(-D*RHO)+E
AA A BB B CC C DD D
E
GD 25.071 2.253 19.080 0.182 13.852 12.933 3.545 101.398
2.420
IMAGINARY PART OF THE ATOMIC SCATTERING FACTORS
GD 12.000
CORRECTLY POSITIONED ATOM(S) FOR WILSON STATISTICS:
GD -0.0010 -0.0040 -0.0030 1.0000
CORRECTLY POSITIONED ATOM(S) FOR WILSON STATISTICS:
GD 0.7110 0.2340 0.2770 1.0000
CORRECTLY POSITIONED ATOM(S) FOR WILSON STATISTICS:
GD 0.7890 0.5300 0.5750 1.0000
CORRECTLY POSITIONED ATOM(S) FOR WILSON STATISTICS:
GD 0.0740 0.7680 0.2960 1.0000
CORRECTLY POSITIONED ATOM(S) FOR WILSON STATISTICS:
GD 0.0770 0.5340 0.2940 1.0000
CORRECTLY POSITIONED ATOM(S) FOR WILSON STATISTICS:
GD 0.7870 0.7640 0.5830 1.0000
CORRECTLY POSITIONED ATOM(S) FOR WILSON STATISTICS:
GD 0.2510 0.7170 0.7360 1.0000
CORRECTLY POSITIONED ATOM(S) FOR WILSON STATISTICS:
GD 0.4400 0.5180 0.5290 1.0000
fmt: read unexpected character
apparent state: unit 9 named /tmp/vanessa/oasis_protdt.31289
last format: (1X,3I4,F7.1,F8.4,F11.3,F7.3,F7.1,F7.2)
lately reading sequential formatted external IO
./oasis.exam: line 30: 31289 Abandon oasis hklin
toto.mtz hklout oasis_8_Gd.mtz <<!
TITLE OAS phasing using Gd derivative
CELL 110.755 137.318 143.419 86.868 73.995 86.014
CON C 37312 N 8960 O 10496 S 224 GD 8
HCO GD 8
SPG P 1
FIT
LCE 20
KMIN 0.05
CYC 1
ANO GD 12
POS GD -0.001 -0.004 -0.003
POS GD 0.711 0.234 0.277
POS GD 0.789 0.530 0.575
POS GD 0.074 0.768 0.296
POS GD 0.077 0.534 0.294
POS GD 0.787 0.764 0.583
POS GD 0.251 0.717 0.736
POS GD 0.440 0.518 0.529
LABIN F1=FP SIGF1=SIGFP F2=DANO SIGF2=SIGDANO
LABOUT F1=FP SIGF1=SIGFP PHI=PHIdp W=Wdp
RES 3.0
END
!
--
Vanessa DELFOSSE -- Doctorante
CHU Pitié Salpêtrière, Université Paris 6
Laboratoire de Recherche Moléculaire sur les Antibiotiques - INSERM U655
91, bd de l'Hôpital
75013 PARIS
Tel : (33) 1 40 77 95 56
Fax : (33) 1 45 82 75 77
[EMAIL PROTECTED]
