Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 6 06:27:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf5_31947/10_2023/7vf5_31947.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf5_31947/10_2023/7vf5_31947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf5_31947/10_2023/7vf5_31947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf5_31947/10_2023/7vf5_31947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf5_31947/10_2023/7vf5_31947.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf5_31947/10_2023/7vf5_31947.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 7760 2.51 5 N 2076 2.21 5 O 2404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 426": "OD1" <-> "OD2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 926": "OE1" <-> "OE2" Residue "A ASP 1186": "OD1" <-> "OD2" Residue "A PHE 1386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 12313 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9325 Classifications: {'peptide': 1188} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1141} Chain breaks: 3 Chain: "C" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1494 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "D" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1494 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Time building chain proxies: 6.73, per 1000 atoms: 0.55 Number of scatterers: 12313 At special positions: 0 Unit cell: (104.96, 111.52, 144.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 2404 8.00 N 2076 7.00 C 7760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 3 sheets defined 76.8% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 373 through 392 removed outlier: 4.251A pdb=" N GLY A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 406 through 421 removed outlier: 4.530A pdb=" N ILE A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 440 Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.687A pdb=" N ALA A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.553A pdb=" N GLU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 4.215A pdb=" N GLY A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 491 removed outlier: 4.016A pdb=" N GLU A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 513 removed outlier: 3.598A pdb=" N LYS A 500 " --> pdb=" O SER A 496 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 529 through 539 Processing helix chain 'A' and resid 543 through 577 removed outlier: 3.635A pdb=" N THR A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 640 removed outlier: 3.925A pdb=" N LEU A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 668 through 679 removed outlier: 3.815A pdb=" N ARG A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 691 through 697 removed outlier: 4.012A pdb=" N HIS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 removed outlier: 4.032A pdb=" N LEU A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 702 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 714 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.738A pdb=" N LEU A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 750 Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.592A pdb=" N PHE A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 780 " --> pdb=" O SER A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 801 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 805 through 816 Processing helix chain 'A' and resid 822 through 832 removed outlier: 3.609A pdb=" N LEU A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 862 Processing helix chain 'A' and resid 865 through 882 removed outlier: 3.743A pdb=" N GLU A 869 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN A 870 " --> pdb=" O GLN A 866 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ALA A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A 874 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 895 removed outlier: 3.761A pdb=" N GLU A 890 " --> pdb=" O ALA A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 907 through 918 Processing helix chain 'A' and resid 928 through 941 removed outlier: 4.234A pdb=" N THR A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 966 removed outlier: 3.587A pdb=" N LEU A 958 " --> pdb=" O LEU A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 983 removed outlier: 3.867A pdb=" N VAL A 975 " --> pdb=" O THR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 989 removed outlier: 3.682A pdb=" N ARG A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1019 removed outlier: 3.844A pdb=" N GLU A1019 " --> pdb=" O THR A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1046 removed outlier: 4.198A pdb=" N THR A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A1042 " --> pdb=" O VAL A1038 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1070 removed outlier: 3.954A pdb=" N LYS A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A1060 " --> pdb=" O ASP A1056 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1091 through 1100 Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1108 through 1120 removed outlier: 3.695A pdb=" N GLU A1118 " --> pdb=" O ILE A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1153 removed outlier: 3.600A pdb=" N ILE A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A1153 " --> pdb=" O MET A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1165 removed outlier: 3.699A pdb=" N GLU A1160 " --> pdb=" O LYS A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1184 removed outlier: 3.628A pdb=" N VAL A1182 " --> pdb=" O ARG A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1208 removed outlier: 3.850A pdb=" N ILE A1195 " --> pdb=" O THR A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1234 Processing helix chain 'A' and resid 1235 through 1247 Processing helix chain 'A' and resid 1253 through 1269 Processing helix chain 'A' and resid 1275 through 1292 removed outlier: 4.024A pdb=" N GLU A1281 " --> pdb=" O GLN A1277 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR A1282 " --> pdb=" O GLN A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1313 Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'A' and resid 1319 through 1336 Processing helix chain 'A' and resid 1340 through 1355 removed outlier: 3.631A pdb=" N LEU A1344 " --> pdb=" O SER A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1371 removed outlier: 3.837A pdb=" N ARG A1369 " --> pdb=" O LYS A1365 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS A1370 " --> pdb=" O SER A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1385 removed outlier: 3.502A pdb=" N THR A1385 " --> pdb=" O ARG A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1404 removed outlier: 3.652A pdb=" N ALA A1394 " --> pdb=" O THR A1390 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1442 Processing helix chain 'A' and resid 1447 through 1462 removed outlier: 3.606A pdb=" N LEU A1459 " --> pdb=" O GLU A1455 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A1460 " --> pdb=" O LEU A1456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1461 " --> pdb=" O GLU A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1486 removed outlier: 4.009A pdb=" N ASP A1471 " --> pdb=" O ASP A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1514 Processing helix chain 'A' and resid 1554 through 1559 removed outlier: 4.304A pdb=" N LYS A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS A1559 " --> pdb=" O LEU A1555 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1554 through 1559' Processing helix chain 'A' and resid 1565 through 1572 removed outlier: 4.131A pdb=" N LEU A1569 " --> pdb=" O LEU A1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 98 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 114 through 146 Processing helix chain 'C' and resid 151 through 176 Processing helix chain 'C' and resid 176 through 244 Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'D' and resid 65 through 98 removed outlier: 4.200A pdb=" N SER D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 145 Processing helix chain 'D' and resid 148 through 176 removed outlier: 3.561A pdb=" N SER D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 247 removed outlier: 3.835A pdb=" N GLU D 184 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER D 247 " --> pdb=" O GLN D 243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 657 through 658 Processing sheet with id=AA2, first strand: chain 'A' and resid 1126 through 1128 removed outlier: 5.904A pdb=" N MET A1126 " --> pdb=" O VAL A1519 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1549 through 1551 838 hydrogen bonds defined for protein. 2505 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.05 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4058 1.34 - 1.46: 1213 1.46 - 1.57: 7101 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 12489 Sorted by residual: bond pdb=" CA LEU A1552 " pdb=" CB LEU A1552 " ideal model delta sigma weight residual 1.525 1.550 -0.026 1.47e-02 4.63e+03 3.04e+00 bond pdb=" C VAL A1033 " pdb=" N PRO A1034 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.28e+00 bond pdb=" CG GLU A 380 " pdb=" CD GLU A 380 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 1.91e+00 bond pdb=" CD GLU A 380 " pdb=" OE1 GLU A 380 " ideal model delta sigma weight residual 1.249 1.223 0.026 1.90e-02 2.77e+03 1.80e+00 bond pdb=" CG1 ILE A 855 " pdb=" CD1 ILE A 855 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.80e+00 ... (remaining 12484 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.51: 209 105.51 - 112.64: 6745 112.64 - 119.78: 4352 119.78 - 126.91: 5463 126.91 - 134.05: 107 Bond angle restraints: 16876 Sorted by residual: angle pdb=" N ILE A 624 " pdb=" CA ILE A 624 " pdb=" C ILE A 624 " ideal model delta sigma weight residual 111.90 108.57 3.33 8.10e-01 1.52e+00 1.69e+01 angle pdb=" N GLU A 380 " pdb=" CA GLU A 380 " pdb=" CB GLU A 380 " ideal model delta sigma weight residual 110.39 116.98 -6.59 1.66e+00 3.63e-01 1.58e+01 angle pdb=" C ILE A 379 " pdb=" N GLU A 380 " pdb=" CA GLU A 380 " ideal model delta sigma weight residual 120.72 114.10 6.62 1.67e+00 3.59e-01 1.57e+01 angle pdb=" C PHE A1400 " pdb=" N MET A1401 " pdb=" CA MET A1401 " ideal model delta sigma weight residual 120.38 124.83 -4.45 1.37e+00 5.33e-01 1.05e+01 angle pdb=" N ILE D 180 " pdb=" CA ILE D 180 " pdb=" C ILE D 180 " ideal model delta sigma weight residual 112.80 109.13 3.67 1.15e+00 7.56e-01 1.02e+01 ... (remaining 16871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7047 17.95 - 35.89: 560 35.89 - 53.84: 116 53.84 - 71.78: 35 71.78 - 89.73: 11 Dihedral angle restraints: 7769 sinusoidal: 3193 harmonic: 4576 Sorted by residual: dihedral pdb=" CA GLN A1443 " pdb=" C GLN A1443 " pdb=" N SER A1444 " pdb=" CA SER A1444 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA HIS A1463 " pdb=" C HIS A1463 " pdb=" N SER A1464 " pdb=" CA SER A1464 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA SER A 965 " pdb=" C SER A 965 " pdb=" N ALA A 966 " pdb=" CA ALA A 966 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 7766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1474 0.043 - 0.086: 439 0.086 - 0.128: 69 0.128 - 0.171: 6 0.171 - 0.214: 3 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CB ILE A1250 " pdb=" CA ILE A1250 " pdb=" CG1 ILE A1250 " pdb=" CG2 ILE A1250 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CG LEU A 689 " pdb=" CB LEU A 689 " pdb=" CD1 LEU A 689 " pdb=" CD2 LEU A 689 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CB VAL A 865 " pdb=" CA VAL A 865 " pdb=" CG1 VAL A 865 " pdb=" CG2 VAL A 865 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.87e-01 ... (remaining 1988 not shown) Planarity restraints: 2168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 447 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO A 448 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 448 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 448 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1504 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A1505 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A1505 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1505 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 145 " -0.012 2.00e-02 2.50e+03 1.34e-02 4.46e+00 pdb=" CG TRP C 145 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP C 145 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP C 145 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 145 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 145 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 145 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 145 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 145 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 145 " 0.001 2.00e-02 2.50e+03 ... (remaining 2165 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 548 2.73 - 3.27: 13115 3.27 - 3.81: 20562 3.81 - 4.36: 24564 4.36 - 4.90: 42391 Nonbonded interactions: 101180 Sorted by model distance: nonbonded pdb=" O ILE A 449 " pdb=" OG SER C 220 " model vdw 2.182 2.440 nonbonded pdb=" OE2 GLU A 518 " pdb=" OH TYR A 560 " model vdw 2.213 2.440 nonbonded pdb=" O GLY D 126 " pdb=" NE2 GLN D 130 " model vdw 2.219 2.520 nonbonded pdb=" OG SER A1507 " pdb=" OD1 ASN A1510 " model vdw 2.220 2.440 nonbonded pdb=" O LEU A1459 " pdb=" OG SER A1464 " model vdw 2.233 2.440 ... (remaining 101175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.410 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 34.520 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12489 Z= 0.215 Angle : 0.637 10.656 16876 Z= 0.351 Chirality : 0.040 0.214 1991 Planarity : 0.004 0.059 2168 Dihedral : 14.392 89.727 4773 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1544 helix: 1.01 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -1.31 (0.30), residues: 416 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.546 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 1.1250 time to fit residues: 196.7913 Evaluate side-chains 100 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 46 optimal weight: 0.0270 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.0770 chunk 139 optimal weight: 10.0000 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 542 GLN ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12489 Z= 0.210 Angle : 0.581 9.676 16876 Z= 0.283 Chirality : 0.038 0.156 1991 Planarity : 0.004 0.057 2168 Dihedral : 4.239 19.238 1639 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.27 % Allowed : 7.74 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1544 helix: 1.23 (0.16), residues: 1163 sheet: None (None), residues: 0 loop : -1.42 (0.31), residues: 381 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 9 residues processed: 145 average time/residue: 1.0713 time to fit residues: 171.9615 Evaluate side-chains 118 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.1136 time to fit residues: 3.3115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 GLN C 65 GLN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.087 12489 Z= 0.649 Angle : 0.828 13.123 16876 Z= 0.402 Chirality : 0.048 0.222 1991 Planarity : 0.005 0.057 2168 Dihedral : 4.861 21.979 1639 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.62 % Allowed : 11.43 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1544 helix: 0.42 (0.15), residues: 1161 sheet: None (None), residues: 0 loop : -1.64 (0.30), residues: 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 115 time to evaluate : 1.459 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 18 residues processed: 149 average time/residue: 1.1174 time to fit residues: 184.4944 Evaluate side-chains 120 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 8 average time/residue: 0.2825 time to fit residues: 5.1097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 419 GLN ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12489 Z= 0.218 Angle : 0.594 9.881 16876 Z= 0.289 Chirality : 0.038 0.139 1991 Planarity : 0.004 0.060 2168 Dihedral : 4.433 19.580 1639 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.77 % Allowed : 14.20 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1544 helix: 1.00 (0.15), residues: 1163 sheet: None (None), residues: 0 loop : -1.48 (0.31), residues: 381 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 110 time to evaluate : 1.428 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 13 residues processed: 139 average time/residue: 0.9741 time to fit residues: 151.7128 Evaluate side-chains 117 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 2 average time/residue: 0.8219 time to fit residues: 3.8906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 110 optimal weight: 0.0770 chunk 61 optimal weight: 0.4980 chunk 127 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 37 optimal weight: 8.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 ASN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12489 Z= 0.203 Angle : 0.562 10.367 16876 Z= 0.274 Chirality : 0.037 0.129 1991 Planarity : 0.004 0.058 2168 Dihedral : 4.246 19.033 1639 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.05 % Allowed : 15.06 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1544 helix: 1.25 (0.16), residues: 1160 sheet: None (None), residues: 0 loop : -1.45 (0.31), residues: 384 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 109 time to evaluate : 1.366 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 21 residues processed: 139 average time/residue: 1.0495 time to fit residues: 162.6984 Evaluate side-chains 120 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 7 average time/residue: 0.4529 time to fit residues: 5.9248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 0.0870 chunk 78 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12489 Z= 0.203 Angle : 0.567 11.219 16876 Z= 0.273 Chirality : 0.037 0.125 1991 Planarity : 0.004 0.060 2168 Dihedral : 4.140 18.688 1639 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.49 % Allowed : 15.98 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.22), residues: 1544 helix: 1.40 (0.16), residues: 1158 sheet: None (None), residues: 0 loop : -1.37 (0.31), residues: 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 1.337 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 134 average time/residue: 1.0622 time to fit residues: 159.1771 Evaluate side-chains 119 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.6059 time to fit residues: 4.2765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 GLN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12489 Z= 0.203 Angle : 0.574 11.550 16876 Z= 0.274 Chirality : 0.037 0.124 1991 Planarity : 0.003 0.058 2168 Dihedral : 4.089 18.573 1639 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.41 % Allowed : 17.47 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.22), residues: 1544 helix: 1.44 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.25 (0.32), residues: 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 101 time to evaluate : 1.326 Fit side-chains outliers start: 34 outliers final: 16 residues processed: 129 average time/residue: 0.9995 time to fit residues: 144.4146 Evaluate side-chains 113 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.371 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.2271 time to fit residues: 2.6751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 0.2980 chunk 29 optimal weight: 0.0000 chunk 28 optimal weight: 0.0070 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 116 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12489 Z= 0.157 Angle : 0.574 12.052 16876 Z= 0.271 Chirality : 0.036 0.120 1991 Planarity : 0.004 0.060 2168 Dihedral : 3.968 17.943 1639 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.27 % Allowed : 17.68 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.22), residues: 1544 helix: 1.67 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.15 (0.31), residues: 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 1.487 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 129 average time/residue: 0.9329 time to fit residues: 136.0544 Evaluate side-chains 112 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.2743 time to fit residues: 2.3163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12489 Z= 0.420 Angle : 0.705 13.072 16876 Z= 0.333 Chirality : 0.042 0.136 1991 Planarity : 0.004 0.058 2168 Dihedral : 4.348 19.588 1639 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.06 % Allowed : 18.54 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.21), residues: 1544 helix: 1.22 (0.15), residues: 1159 sheet: None (None), residues: 0 loop : -1.31 (0.31), residues: 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 1.346 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 124 average time/residue: 1.0567 time to fit residues: 146.7227 Evaluate side-chains 114 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.469 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.2069 time to fit residues: 3.2411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 141 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12489 Z= 0.218 Angle : 0.623 13.656 16876 Z= 0.293 Chirality : 0.037 0.139 1991 Planarity : 0.004 0.059 2168 Dihedral : 4.187 19.055 1639 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.56 % Allowed : 19.39 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.22), residues: 1544 helix: 1.51 (0.16), residues: 1152 sheet: None (None), residues: 0 loop : -1.22 (0.31), residues: 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 1.446 Fit side-chains outliers start: 22 outliers final: 17 residues processed: 114 average time/residue: 1.0111 time to fit residues: 129.6234 Evaluate side-chains 110 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 1.292 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.2720 time to fit residues: 2.3864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.0470 chunk 122 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.212143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.133234 restraints weight = 14008.133| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.97 r_work: 0.3706 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12489 Z= 0.329 Angle : 0.660 13.289 16876 Z= 0.311 Chirality : 0.040 0.131 1991 Planarity : 0.004 0.058 2168 Dihedral : 4.275 19.600 1639 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.42 % Allowed : 19.60 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.22), residues: 1544 helix: 1.33 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -1.17 (0.32), residues: 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3474.51 seconds wall clock time: 63 minutes 19.39 seconds (3799.39 seconds total)