Dear all,
I have refined a 2.5 A structure (P212121, a=29, b=56, c=58) with
Refmac/TLS to an R/Rfree of 20.9/23.7. Everything seems to run
smoothly, maps look nice. Total B-facors for protein (residual+TLS)
after TLSANL are in the 25 to 50 A^2 range.
However, water B-factors are refined to unreasonably low values, many
hitting bottom at 2.0 A^2.
A refmac refinement without TLS easily fixes the water B-factors to
reasonable values, but gives 2-3% higher R-factors. (I have attached
the relavant parts of the PDB file from TLSANL)
Thanks for your help.
Clemens
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HEADER ----XX-XXX-XX xxxx
COMPND --REMARK 3
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0072
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.44
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.00
REMARK 3 NUMBER OF REFLECTIONS : 3709
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.20987
REMARK 3 R VALUE (WORKING SET) : 0.20853
REMARK 3 FREE R VALUE : 0.23739
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.5
REMARK 3 FREE R VALUE TEST SET COUNT : 176
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH : 2.436
REMARK 3 BIN RESOLUTION RANGE LOW : 2.498
REMARK 3 REFLECTION IN BIN (WORKING SET) : 257
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00
REMARK 3 BIN R VALUE (WORKING SET) : 0.270
REMARK 3 BIN FREE R VALUE SET COUNT : 12
REMARK 3 BIN FREE R VALUE : 0.447
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 ALL ATOMS : 739
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.763
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.79
REMARK 3 B22 (A**2) : 0.73
REMARK 3 B33 (A**2) : 0.06
REMARK 3 B12 (A**2) : 0.00
REMARK 3 B13 (A**2) : 0.00
REMARK 3 B23 (A**2) : 0.00
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.511
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.262
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.200
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.990
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 708 ; 0.007 ; 0.022
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 961 ; 1.025 ; 1.997
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 89 ; 4.288 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 28 ;27.435 ;26.429
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 126 ;16.669 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ;26.600 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 114 ; 0.063 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 515 ; 0.003 ; 0.022
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 457 ; 0.230 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 734 ; 0.465 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 251 ; 0.796 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 227 ; 1.426 ; 4.500
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 TWIN DETAILS
REMARK 3 NUMBER OF TWIN DOMAINS : NULL
REMARK 3
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 3
REMARK 3 ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
REMARK 3 ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 544 A 602
REMARK 3 ORIGIN FOR THE GROUP (A): -1.5600 2.1310 -6.4040
REMARK 3 T TENSOR
REMARK 3 T11: 0.1987 T22: 0.1032
REMARK 3 T33: 0.3334 T12: 0.0148
REMARK 3 T13: 0.0192 T23: 0.0107
REMARK 3 L TENSOR
REMARK 3 L11: 3.0232 L22: 9.5047
REMARK 3 L33: 4.8404 L12: -1.4527
REMARK 3 L13: -0.6037 L23: 4.9346
REMARK 3 S TENSOR
REMARK 3 S11: -0.1419 S12: 0.1446 S13: -0.3926
REMARK 3 S21: 0.0466 S22: 0.1236 S23: 0.3172
REMARK 3 S31: 0.5765 S32: 0.0337 S33: 0.0183
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 603 A 618
REMARK 3 ORIGIN FOR THE GROUP (A): -1.8300 16.9090 -10.8800
REMARK 3 T TENSOR
REMARK 3 T11: 0.3257 T22: 0.1237
REMARK 3 T33: 0.5111 T12: 0.0425
REMARK 3 T13: 0.1163 T23: 0.0512
REMARK 3 L TENSOR
REMARK 3 L11: 1.6795 L22: 8.6130
REMARK 3 L33: 12.8859 L12: -2.8217
REMARK 3 L13: 2.6868 L23: -6.1187
REMARK 3 S TENSOR
REMARK 3 S11: 0.3353 S12: 0.0667 S13: 0.6777
REMARK 3 S21: -1.1822 S22: -0.2639 S23: -0.3889
REMARK 3 S31: -0.1764 S32: -0.3374 S33: -0.0715
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B 55 B 70
REMARK 3 ORIGIN FOR THE GROUP (A): -14.5620 8.6240 -5.7360
REMARK 3 T TENSOR
REMARK 3 T11: 0.1819 T22: 0.1925
REMARK 3 T33: 0.3593 T12: 0.0608
REMARK 3 T13: -0.1222 T23: -0.0613
REMARK 3 L TENSOR
REMARK 3 L11: 17.1809 L22: 8.0907
REMARK 3 L33: 11.5783 L12: 4.7167
REMARK 3 L13: -8.6740 L23: -5.2009
REMARK 3 S TENSOR
REMARK 3 S11: -0.3434 S12: 0.1788 S13: -0.1980
REMARK 3 S21: -0.5824 S22: 0.2303 S23: 0.3357
REMARK 3 S31: 0.1582 S32: -1.1131 S33: 0.1131
REMARK 3
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
REMARK 3 U VALUES : RESIDUAL ONLY
REMARK 3
CRYST1 29.110 56.860 58.030 90.00 90.00 90.00 P 21 21 21
SCALE1 0.034352 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017587 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017232 0.00000
ATOM 1 N PRO A 544 4.309 -5.412 0.830 1.00 48.24 N
ANISOU 1 N PRO A 544 8944 3209 6175 0 0 0 N
ATOM 2 CA PRO A 544 5.330 -5.406 -0.215 1.00 47.23 C
ANISOU 2 CA PRO A 544 8267 3324 6355 0 0 0 C
ATOM 3 CB PRO A 544 6.497 -6.154 0.445 1.00 51.83 C
ANISOU 3 CB PRO A 544 9168 3699 6824 0 0 0 C
ATOM 4 CG PRO A 544 5.844 -7.034 1.542 1.00 55.52 C
ANISOU 4 CG PRO A 544 10558 3665 6872 0 0 0 C
ATOM 5 CD PRO A 544 4.395 -6.616 1.678 1.00 53.15 C
ANISOU 5 CD PRO A 544 10367 3339 6487 0 0 0 C
ATOM 6 C PRO A 544 4.854 -6.130 -1.486 1.00 45.86 C
ANISOU 6 C PRO A 544 7943 3090 6392 0 0 0 C
ATOM 7 O PRO A 544 5.152 -7.314 -1.678 1.00 48.59 O
ANISOU 7 O PRO A 544 8563 3153 6744 0 0 0 O
ATOM 8 N LEU A 545 4.115 -5.416 -2.337 1.00 41.94 N
ANISOU 8 N LEU A 545 7046 2838 6050 0 0 0 N
ATOM 9 CA LEU A 545 3.521 -5.995 -3.551 1.00 40.40 C
ANISOU 9 CA LEU A 545 6722 2604 6023 0 0 0 C
ATOM 10 CB LEU A 545 2.454 -5.062 -4.131 1.00 37.30 C
ANISOU 10 CB LEU A 545 6025 2433 5713 0 0 0 C
ATOM 11 CG LEU A 545 0.971 -5.409 -4.033 1.00 37.29 C
ANISOU 11 CG LEU A 545 6198 2227 5744 0 0 0 C
ATOM 12 CD1 LEU A 545 0.169 -4.308 -4.687 1.00 34.32 C
ANISOU 12 CD1 LEU A 545 5425 2133 5480 0 0 0 C
ATOM 13 CD2 LEU A 545 0.674 -6.739 -4.700 1.00 39.63 C
ANISOU 13 CD2 LEU A 545 6657 2245 6155 0 0 0 C
ATOM 14 C LEU A 545 4.532 -6.296 -4.647 1.00 40.30 C
ANISOU 14 C LEU A 545 6394 2731 6189 0 0 0 C
ATOM 15 O LEU A 545 5.296 -5.415 -5.049 1.00 39.28 O
ANISOU 15 O LEU A 545 5851 2912 6160 0 0 0 O
[.............................................................................]
ATOM 721 O HOH Z 26 4.331 15.110 2.443 1.00 2.00 O
ATOM 722 O HOH Z 27 1.264 -6.899 -12.249 1.00 2.00 O
ATOM 723 O HOH Z 28 -16.512 7.213 -5.802 1.00 2.00 O
ATOM 724 O HOH Z 29 10.966 0.572 -2.021 1.00 2.00 O
ATOM 725 O HOH Z 30 -1.212 -6.621 -13.323 1.00 14.85 O
ATOM 726 O HOH Z 31 -3.187 -8.577 -15.238 1.00 2.00 O
ATOM 727 O HOH Z 32 1.541 19.977 -9.823 1.00 2.00 O
ATOM 728 O HOH Z 33 -18.041 1.731 2.138 1.00 2.00 O
ATOM 729 O HOH Z 34 -15.674 13.690 -10.888 1.00 10.07 O
ATOM 730 O HOH Z 35 -6.429 9.025 -15.088 1.00 2.00 O
ATOM 731 OW0 HOH Z 36 -8.068 11.911 2.520 1.00 2.00 O
ATOM 732 OW0 HOH Z 37 -8.131 21.050 1.317 1.00 2.94 O
ATOM 733 OW0 HOH Z 38 7.360 -10.570 -9.323 1.00 2.00 O
ATOM 734 OW0 HOH Z 39 -3.377 -10.981 -14.550 1.00 2.00 O
ATOM 735 OW0 HOH Z 40 -10.173 19.052 -0.857 1.00 13.04 O
ATOM 736 OW0 HOH Z 41 -12.070 1.106 -0.308 1.00 2.00 O
ATOM 737 OW0 HOH Z 42 -13.008 21.323 -8.964 1.00 2.00 O
ATOM 738 OW0 HOH Z 43 2.014 -2.216 -18.360 1.00 23.56 O
ATOM 739 OW0 HOH Z 45 -9.727 -3.842 -8.213 1.00 7.42 O
END
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Dr. Clemens Grimm
Institut für Biochemie
Biozentrum der Universität Würzburg
Am Hubland
D-97074 Würzburg
Germany
e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
phone : +49 0931 888 84031
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