Starting phenix.real_space_refine on Tue Sep 15 01:00:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5m5x_3447/09_2026/5m5x_3447_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5m5x_3447/09_2026/5m5x_3447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5m5x_3447/09_2026/5m5x_3447_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5m5x_3447/09_2026/5m5x_3447_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5m5x_3447/09_2026/5m5x_3447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5m5x_3447/09_2026/5m5x_3447.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 79 5.49 5 S 167 5.16 5 C 21569 2.51 5 N 5992 2.21 5 O 6678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34491 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1455, 11488 Classifications: {'peptide': 1455} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1395} Chain breaks: 8 Chain: "B" Number of atoms: 9301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9301 Classifications: {'peptide': 1170} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1110} Chain breaks: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1751 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1486 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 3 Chain: "H" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1075 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 472 Classifications: {'peptide': 64} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 60} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "L" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'TRANS': 42} Chain: "M" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 802 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain breaks: 1 Chain: "N" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1070 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 125} Chain breaks: 3 Chain: "R" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 281 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain: "S" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 579 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "T" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 774 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 781 SG CYS A 102 72.684 101.508 33.719 1.00 54.13 S ATOM 806 SG CYS A 105 74.987 99.958 31.809 1.00 52.73 S ATOM 1609 SG CYS A 233 76.859 102.766 33.805 1.00 50.62 S ATOM 1631 SG CYS A 236 74.633 102.585 30.730 1.00 55.36 S ATOM 461 SG CYS A 62 64.303 53.859 52.063 1.00 44.35 S ATOM 480 SG CYS A 65 67.229 51.791 52.507 1.00 39.83 S ATOM 535 SG CYS A 72 67.745 53.657 54.510 1.00 42.32 S ATOM 20069 SG CYS B1104 80.770 59.495 43.709 1.00 51.46 S ATOM 20095 SG CYS B1107 79.576 61.789 44.487 1.00 49.98 S ATOM 20242 SG CYS B1128 77.370 59.632 43.891 1.00 43.18 S ATOM 20270 SG CYS B1131 78.637 61.914 40.702 1.00 47.90 S ATOM 28894 SG CYS I 13 43.069 133.477 85.912 1.00 68.90 S ATOM 29014 SG CYS I 30 44.928 132.829 82.668 1.00 70.69 S ATOM 29335 SG CYS J 7 81.314 53.015 123.998 1.00 37.00 S ATOM 29358 SG CYS J 10 82.777 50.792 125.992 1.00 34.83 S ATOM 29638 SG CYS J 45 84.890 53.838 126.063 1.00 33.27 S ATOM 29644 SG CYS J 46 80.635 51.895 127.054 1.00 33.39 S ATOM 30670 SG CYS L 31 40.377 52.291 107.182 1.00 41.61 S ATOM 30690 SG CYS L 34 38.615 51.351 108.660 1.00 42.55 S ATOM 30794 SG CYS L 48 37.310 49.761 106.123 1.00 52.48 S ATOM 30817 SG CYS L 51 37.452 53.730 107.388 1.00 49.47 S Time building chain proxies: 5.96, per 1000 atoms: 0.17 Number of scatterers: 34491 At special positions: 0 Unit cell: (160.65, 163.35, 168.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 167 16.00 P 79 15.00 O 6678 8.00 N 5992 7.00 C 21569 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 - 3.00 Amino acid : True - 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: 2.96 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 27 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7776 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 53 sheets defined 33.4% alpha, 19.4% beta 13 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 4.03 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.644A pdb=" N ILE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.761A pdb=" N GLY A 55 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 removed outlier: 4.007A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 removed outlier: 4.355A pdb=" N TYR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.660A pdb=" N LEU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 225 removed outlier: 3.765A pdb=" N ASN A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 257 through 267 removed outlier: 4.417A pdb=" N ASN A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 removed outlier: 4.139A pdb=" N LYS A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.861A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 382 through 398 removed outlier: 4.118A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.644A pdb=" N LEU A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 removed outlier: 3.893A pdb=" N HIS A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 removed outlier: 3.670A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 505' Processing helix chain 'A' and resid 518 through 526 removed outlier: 3.554A pdb=" N ALA A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 676 through 681 Processing helix chain 'A' and resid 688 through 701 removed outlier: 4.302A pdb=" N GLN A 693 " --> pdb=" O ARG A 689 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 739 Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.964A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 822 removed outlier: 3.751A pdb=" N SER A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 834 removed outlier: 3.593A pdb=" N LEU A 833 " --> pdb=" O MET A 830 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 849 Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.683A pdb=" N THR A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 removed outlier: 3.518A pdb=" N LYS A 877 " --> pdb=" O PRO A 873 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 890 Processing helix chain 'A' and resid 894 through 911 Processing helix chain 'A' and resid 925 through 930 Processing helix chain 'A' and resid 936 through 944 removed outlier: 3.711A pdb=" N VAL A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1013 removed outlier: 3.883A pdb=" N PHE A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1025 removed outlier: 3.820A pdb=" N GLY A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1061 through 1064 removed outlier: 4.306A pdb=" N THR A1064 " --> pdb=" O SER A1061 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1061 through 1064' Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1081 Processing helix chain 'A' and resid 1082 through 1085 Processing helix chain 'A' and resid 1091 through 1109 removed outlier: 3.588A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1116 Processing helix chain 'A' and resid 1138 through 1150 Processing helix chain 'A' and resid 1165 through 1176 Processing helix chain 'A' and resid 1184 through 1192 removed outlier: 3.985A pdb=" N ILE A1188 " --> pdb=" O ALA A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1200 removed outlier: 3.527A pdb=" N THR A1198 " --> pdb=" O GLY A1194 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A1199 " --> pdb=" O GLU A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1228 removed outlier: 3.606A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A1226 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1259 removed outlier: 4.242A pdb=" N THR A1253 " --> pdb=" O GLU A1249 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1265 Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 4.367A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 Processing helix chain 'A' and resid 1320 through 1338 removed outlier: 3.656A pdb=" N GLU A1326 " --> pdb=" O ILE A1322 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A1327 " --> pdb=" O HIS A1323 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A1328 " --> pdb=" O LEU A1324 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A1329 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1454 removed outlier: 3.525A pdb=" N ILE A1450 " --> pdb=" O ARG A1446 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS A1453 " --> pdb=" O ALA A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1481 removed outlier: 3.854A pdb=" N THR A1480 " --> pdb=" O ALA A1477 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A1481 " --> pdb=" O ALA A1478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1477 through 1481' Processing helix chain 'A' and resid 1486 through 1494 removed outlier: 3.886A pdb=" N ILE A1492 " --> pdb=" O ILE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1553 Processing helix chain 'A' and resid 1553 through 1561 removed outlier: 4.169A pdb=" N ALA A1557 " --> pdb=" O TYR A1553 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A1558 " --> pdb=" O GLY A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1572 removed outlier: 3.552A pdb=" N PHE A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.924A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1609 through 1614 Processing helix chain 'A' and resid 1617 through 1627 Processing helix chain 'A' and resid 1649 through 1653 removed outlier: 3.684A pdb=" N SER A1653 " --> pdb=" O GLY A1650 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 42 through 52 removed outlier: 3.787A pdb=" N LEU B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.765A pdb=" N GLY B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 67 removed outlier: 3.526A pdb=" N ASP B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.973A pdb=" N TYR B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 90' Processing helix chain 'B' and resid 122 through 128 removed outlier: 3.640A pdb=" N GLN B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 286 through 292 removed outlier: 4.601A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 315 removed outlier: 3.711A pdb=" N ARG B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 345 through 358 removed outlier: 4.261A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.891A pdb=" N LEU B 362 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 386 removed outlier: 3.780A pdb=" N LEU B 375 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 386 " --> pdb=" O TYR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.882A pdb=" N LEU B 413 " --> pdb=" O TYR B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 429 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 442 through 453 removed outlier: 3.700A pdb=" N MET B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 492 through 501 removed outlier: 3.669A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.724A pdb=" N GLY B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 602 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 704 Processing helix chain 'B' and resid 711 through 723 removed outlier: 3.853A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 761 removed outlier: 3.802A pdb=" N TYR B 760 " --> pdb=" O LEU B 756 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 761' Processing helix chain 'B' and resid 790 through 795 removed outlier: 3.536A pdb=" N ASP B 794 " --> pdb=" O ASN B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 960 through 976 removed outlier: 3.833A pdb=" N SER B 966 " --> pdb=" O MET B 962 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 removed outlier: 3.840A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1082 removed outlier: 3.659A pdb=" N ASP B1077 " --> pdb=" O GLU B1073 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B1078 " --> pdb=" O MET B1074 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N HIS B1082 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1093 removed outlier: 3.549A pdb=" N ARG B1091 " --> pdb=" O LEU B1087 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B1093 " --> pdb=" O GLN B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1192 removed outlier: 3.691A pdb=" N MET B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 60 through 74 removed outlier: 4.077A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.587A pdb=" N ASP C 166 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 311 through 330 removed outlier: 3.597A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 46 removed outlier: 4.113A pdb=" N ASP D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.845A pdb=" N SER D 85 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.676A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU E 21 " --> pdb=" O ARG E 17 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG E 26 " --> pdb=" O MET E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.714A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.645A pdb=" N MET E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 123 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.606A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 56 through 73 removed outlier: 3.533A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.551A pdb=" N GLN F 78 " --> pdb=" O PRO F 75 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 75 through 79' Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 9 through 20 removed outlier: 3.881A pdb=" N HIS G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 66 removed outlier: 3.515A pdb=" N GLY G 60 " --> pdb=" O ASN G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 162 Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.517A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.287A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.646A pdb=" N ALA J 35 " --> pdb=" O ASP J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 51 removed outlier: 3.527A pdb=" N ARG J 48 " --> pdb=" O TYR J 44 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.787A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 140 removed outlier: 3.845A pdb=" N ALA K 116 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE K 135 " --> pdb=" O VAL K 131 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 6.807A pdb=" N ILE A 11 " --> pdb=" O GLU B1201 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLU B1201 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER A 13 " --> pdb=" O ASN B1199 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN B1199 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 77 through 86 removed outlier: 11.389A pdb=" N LEU A 81 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N VAL A 361 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 10.913A pdb=" N VAL A 83 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 359 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 243 through 245 removed outlier: 3.684A pdb=" N GLU A 253 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 371 through 371 No H-bonds generated for sheet with id=AD Processing sheet with id=AE, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.936A pdb=" N LYS A 474 " --> pdb=" O VAL B1071 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 479 through 486 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1045 through 1047 current: chain 'A' and resid 600 through 607 removed outlier: 3.618A pdb=" N MET A 601 " --> pdb=" O MET A 589 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 586 through 590 current: chain 'A' and resid 614 through 616 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 614 through 616 current: chain 'A' and resid 632 through 636 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 632 through 636 current: chain 'A' and resid 479 through 486 Processing sheet with id=AG, first strand: chain 'A' and resid 506 through 510 removed outlier: 6.740A pdb=" N LYS A 576 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE A 536 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N TYR A 578 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR A 534 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'A' and resid 686 through 687 removed outlier: 3.728A pdb=" N PHE A 687 " --> pdb=" O TRP A 726 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'A' and resid 719 through 721 removed outlier: 6.665A pdb=" N VAL H 96 " --> pdb=" O PHE A 720 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 95 through 106 current: chain 'H' and resid 54 through 60 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 54 through 60 current: chain 'H' and resid 54 through 60 Processing sheet with id=AJ, first strand: chain 'A' and resid 749 through 752 removed outlier: 7.230A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 777 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'A' and resid 826 through 827 removed outlier: 5.765A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 1010 through 1011 removed outlier: 3.846A pdb=" N ILE B1026 " --> pdb=" O GLU B1011 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'A' and resid 948 through 949 removed outlier: 4.981A pdb=" N GLY A 948 " --> pdb=" O VAL A 982 " (cutoff:3.500A) Processing sheet with id=AM, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 7.253A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AN, first strand: chain 'A' and resid 1504 through 1508 removed outlier: 3.876A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A1238 " --> pdb=" O THR A1521 " (cutoff:3.500A) Processing sheet with id=AO, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.852A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AP, first strand: chain 'A' and resid 1457 through 1462 removed outlier: 5.994A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER A1289 " --> pdb=" O GLU A1274 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU A1274 " --> pdb=" O SER A1289 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A1291 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL A1272 " --> pdb=" O VAL A1291 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N HIS A1293 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A1270 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG A1295 " --> pdb=" O ASP A1268 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 21 through 24 removed outlier: 4.464A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) Processing sheet with id=DB, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.724A pdb=" N GLN D 29 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG G 40 " --> pdb=" O GLN D 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=DB Processing sheet with id=FA, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.182A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE G 107 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL G 81 " --> pdb=" O LYS G 72 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS G 72 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id=FB, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.182A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE G 107 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG G 40 " --> pdb=" O GLN D 29 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN D 29 " --> pdb=" O ARG G 40 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'B' and resid 71 through 74 removed outlier: 4.957A pdb=" N VAL B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N SER B 144 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 145 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU B 150 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.504A pdb=" N ASP B 111 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N VAL B 117 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing sheet with id=BD, first strand: chain 'B' and resid 194 through 196 removed outlier: 3.523A pdb=" N LEU B 202 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing sheet with id=BE, first strand: chain 'B' and resid 400 through 403 removed outlier: 3.601A pdb=" N LEU B 206 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N MET B 205 " --> pdb=" O MET B 502 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS B 504 " --> pdb=" O MET B 205 " (cutoff:3.500A) Processing sheet with id=BF, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.725A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS B 251 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 259 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 262 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN B 267 " --> pdb=" O TRP B 264 " (cutoff:3.500A) Processing sheet with id=BG, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=BH, first strand: chain 'B' and resid 660 through 664 Processing sheet with id=BI, first strand: chain 'B' and resid 674 through 675 Processing sheet with id=BJ, first strand: chain 'B' and resid 674 through 675 Processing sheet with id=BK, first strand: chain 'B' and resid 571 through 572 removed outlier: 4.080A pdb=" N ALA B 571 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TRP B 595 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 594 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 596 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU B 625 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=BL, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.749A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=BM, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.749A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=BN, first strand: chain 'B' and resid 752 through 753 removed outlier: 3.934A pdb=" N LYS B 753 " --> pdb=" O GLN B 979 " (cutoff:3.500A) No H-bonds generated for sheet with id=BN Processing sheet with id=BO, first strand: chain 'B' and resid 823 through 825 removed outlier: 4.082A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) Processing sheet with id=BP, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=BQ, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=BR, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=BS, first strand: chain 'B' and resid 1133 through 1134 removed outlier: 3.598A pdb=" N TRP B1159 " --> pdb=" O PHE B1167 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.783A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 10.205A pdb=" N LEU C 291 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N ILE C 235 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ARG C 293 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE C 233 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N ARG C 295 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N HIS C 297 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU C 229 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE C 299 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR C 227 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.238A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 132 " --> pdb=" O CYS C 208 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLU C 201 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ASN C 87 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 211 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=CD, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.742A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=CE, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=EA, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.713A pdb=" N PHE E 60 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE E 110 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 87 through 88 removed outlier: 4.469A pdb=" N VAL E 88 " --> pdb=" O ASN E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=EB Processing sheet with id=EC, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.423A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE E 199 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id=GA, first strand: chain 'G' and resid 132 through 140 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 228 through 237 current: chain 'G' and resid 153 through 158 Processing sheet with id=GB, first strand: chain 'G' and resid 167 through 170 Processing sheet with id=IA, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=KA, first strand: chain 'K' and resid 47 through 49 removed outlier: 6.822A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id=NA, first strand: chain 'N' and resid 69 through 71 removed outlier: 6.781A pdb=" N LEU M 90 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL M 15 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LYS M 92 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLN M 89 " --> pdb=" O LEU M 80 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU M 80 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS N 135 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU N 55 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL N 139 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N GLU N 141 " --> pdb=" O PRO N 59 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE N 82 " --> pdb=" O HIS N 85 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR N 87 " --> pdb=" O MET N 80 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET N 80 " --> pdb=" O TYR N 87 " (cutoff:3.500A) Processing sheet with id=NB, first strand: chain 'N' and resid 29 through 31 removed outlier: 4.041A pdb=" N LYS N 30 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS M 54 " --> pdb=" O ASP M 39 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL M 52 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU M 53 " --> pdb=" O GLY M 64 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY M 64 " --> pdb=" O LEU M 53 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL M 101 " --> pdb=" O GLU M 61 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA M 22 " --> pdb=" O LEU N 110 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 3051 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 9.31 Time building geometry restraints manager: 3.92 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: 10851 1.34 - 1.46: 5482 1.46 - 1.58: 18563 1.58 - 1.70: 157 1.70 - 1.82: 265 Bond restraints: 35318 Sorted by residual: bond pdb=" N ASP K 57 " pdb=" CA ASP K 57 " ideal model delta sigma weight residual 1.458 1.654 -0.196 1.27e-02 6.20e+03 2.38e+02 bond pdb=" CA GLY K 58 " pdb=" C GLY K 58 " ideal model delta sigma weight residual 1.514 1.386 0.129 1.41e-02 5.03e+03 8.31e+01 bond pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 1.533 1.664 -0.131 1.58e-02 4.01e+03 6.86e+01 bond pdb=" N LYS B1064 " pdb=" CA LYS B1064 " ideal model delta sigma weight residual 1.458 1.563 -0.105 1.30e-02 5.92e+03 6.48e+01 bond pdb=" N GLY A 763 " pdb=" CA GLY A 763 " ideal model delta sigma weight residual 1.449 1.553 -0.104 1.45e-02 4.76e+03 5.13e+01 ... (remaining 35313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.85: 48026 7.85 - 15.70: 19 15.70 - 23.55: 3 23.55 - 31.39: 1 31.39 - 39.24: 2 Bond angle restraints: 48051 Sorted by residual: angle pdb=" N ASP K 57 " pdb=" CA ASP K 57 " pdb=" C ASP K 57 " ideal model delta sigma weight residual 112.68 73.44 39.24 1.33e+00 5.65e-01 8.71e+02 angle pdb=" N LYS B1064 " pdb=" CA LYS B1064 " pdb=" C LYS B1064 " ideal model delta sigma weight residual 113.55 78.50 35.05 1.26e+00 6.30e-01 7.74e+02 angle pdb=" C ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 110.24 85.90 24.34 1.67e+00 3.59e-01 2.12e+02 angle pdb=" N SER A 764 " pdb=" CA SER A 764 " pdb=" C SER A 764 " ideal model delta sigma weight residual 108.54 90.32 18.22 1.41e+00 5.03e-01 1.67e+02 angle pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " pdb=" CG ASP K 57 " ideal model delta sigma weight residual 112.60 102.85 9.75 1.00e+00 1.00e+00 9.50e+01 ... (remaining 48046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 20855 35.00 - 69.99: 471 69.99 - 104.99: 17 104.99 - 139.98: 0 139.98 - 174.98: 3 Dihedral angle restraints: 21346 sinusoidal: 9321 harmonic: 12025 Sorted by residual: dihedral pdb=" C ASP K 57 " pdb=" N ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta harmonic sigma weight residual -122.60 -84.01 -38.59 0 2.50e+00 1.60e-01 2.38e+02 dihedral pdb=" C LYS B1064 " pdb=" N LYS B1064 " pdb=" CA LYS B1064 " pdb=" CB LYS B1064 " ideal model delta harmonic sigma weight residual -122.60 -93.90 -28.70 0 2.50e+00 1.60e-01 1.32e+02 dihedral pdb=" N ASP K 57 " pdb=" C ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta harmonic sigma weight residual 122.80 97.15 25.65 0 2.50e+00 1.60e-01 1.05e+02 ... (remaining 21343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 5372 0.294 - 0.588: 5 0.588 - 0.882: 1 0.882 - 1.176: 1 1.176 - 1.471: 1 Chirality restraints: 5380 Sorted by residual: chirality pdb=" CA ASP K 57 " pdb=" N ASP K 57 " pdb=" C ASP K 57 " pdb=" CB ASP K 57 " both_signs ideal model delta sigma weight residual False 2.51 3.98 -1.47 2.00e-01 2.50e+01 5.41e+01 chirality pdb=" CA LYS B1064 " pdb=" N LYS B1064 " pdb=" C LYS B1064 " pdb=" CB LYS B1064 " both_signs ideal model delta sigma weight residual False 2.51 3.64 -1.13 2.00e-01 2.50e+01 3.17e+01 chirality pdb=" CA ASP A 867 " pdb=" N ASP A 867 " pdb=" C ASP A 867 " pdb=" CB ASP A 867 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 5377 not shown) Planarity restraints: 5924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY K 58 " 0.029 2.00e-02 2.50e+03 5.58e-02 3.11e+01 pdb=" C GLY K 58 " -0.097 2.00e-02 2.50e+03 pdb=" O GLY K 58 " 0.034 2.00e-02 2.50e+03 pdb=" N THR K 59 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 341 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO B 342 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 342 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 342 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 130 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.55e+00 pdb=" N PRO F 131 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 131 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 131 " 0.022 5.00e-02 4.00e+02 ... (remaining 5921 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 181 2.46 - 3.07: 22477 3.07 - 3.68: 52879 3.68 - 4.29: 75776 4.29 - 4.90: 121647 Nonbonded interactions: 272960 Sorted by model distance: nonbonded pdb=" NH1 ARG B 17 " pdb=" OD2 ASP B 758 " model vdw 1.852 3.120 nonbonded pdb=" NH1 ARG A1105 " pdb=" OE2 GLU A1138 " model vdw 1.913 3.120 nonbonded pdb=" NZ LYS A1473 " pdb=" OE2 GLU A1475 " model vdw 1.931 3.120 nonbonded pdb=" O PHE A 248 " pdb=" OG1 THR A 249 " model vdw 1.946 3.040 nonbonded pdb=" N ASP K 57 " pdb=" N GLY K 58 " model vdw 2.005 2.560 ... (remaining 272955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.500 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 38.080 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 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 0.196 35340 Z= 0.206 Angle : 0.885 44.289 48078 Z= 0.432 Chirality : 0.051 1.471 5380 Planarity : 0.004 0.056 5924 Dihedral : 13.163 174.981 13570 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.41 % Favored : 94.39 % Rotamer: Outliers : 1.42 % Allowed : 9.44 % Favored : 89.15 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.57 (0.10), residues: 4063 helix: -3.34 (0.10), residues: 1258 sheet: -2.65 (0.19), residues: 579 loop : -3.00 (0.11), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1063 TYR 0.012 0.001 TYR H 116 PHE 0.011 0.001 PHE E 72 TRP 0.012 0.001 TRP B 836 HIS 0.003 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.20 (35318) covalent geometry : angle 0.65974 / 0.42 (48051) hydrogen bonds : bond 0.19533 / 13.13 ( 1082) hydrogen bonds : angle 10.55818 / 7.20 ( 3115) metal coordination : bond 0.04676 / 3.49 ( 22) metal coordination : angle 24.88773 / 13.82 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 945 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.7751 (mt0) cc_final: 0.7344 (mt0) REVERT: A 458 GLN cc_start: 0.5688 (pm20) cc_final: 0.5395 (pm20) REVERT: A 633 MET cc_start: 0.7111 (ptm) cc_final: 0.6472 (mtm) REVERT: A 642 ASN cc_start: 0.6366 (t0) cc_final: 0.6063 (t0) REVERT: A 658 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7239 (mt) REVERT: A 726 TRP cc_start: 0.6756 (m-90) cc_final: 0.6415 (m-90) REVERT: A 930 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8048 (tt) REVERT: A 1074 TYR cc_start: 0.8256 (m-10) cc_final: 0.8032 (m-80) REVERT: A 1249 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7181 (mm-30) REVERT: A 1457 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6580 (mt) REVERT: A 1503 HIS cc_start: 0.5936 (m-70) cc_final: 0.5678 (m-70) REVERT: A 1508 VAL cc_start: 0.6818 (t) cc_final: 0.6502 (t) REVERT: A 1535 PHE cc_start: 0.6017 (p90) cc_final: 0.5607 (p90) REVERT: A 1553 TYR cc_start: 0.8003 (m-80) cc_final: 0.7766 (m-80) REVERT: A 1588 MET cc_start: 0.7783 (tpt) cc_final: 0.7544 (tpt) REVERT: A 1613 MET cc_start: 0.5634 (mmt) cc_final: 0.5425 (mtp) REVERT: A 1646 LEU cc_start: 0.8224 (mt) cc_final: 0.7986 (mm) REVERT: B 45 HIS cc_start: 0.5594 (m90) cc_final: 0.5362 (m90) REVERT: B 541 LEU cc_start: 0.7067 (mt) cc_final: 0.6284 (pp) REVERT: B 690 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6278 (tt0) REVERT: B 836 TRP cc_start: 0.5808 (p90) cc_final: 0.5496 (p90) REVERT: B 934 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7897 (pp) REVERT: B 935 ASP cc_start: 0.7701 (m-30) cc_final: 0.7122 (t0) REVERT: B 977 ILE cc_start: 0.7917 (tt) cc_final: 0.7410 (tp) REVERT: B 1039 MET cc_start: 0.7322 (tmt) cc_final: 0.6666 (tmt) REVERT: B 1074 MET cc_start: 0.7536 (mmt) cc_final: 0.7277 (mmm) REVERT: B 1133 MET cc_start: 0.5854 (tpp) cc_final: 0.5422 (tpt) REVERT: D 27 LEU cc_start: 0.7366 (mp) cc_final: 0.6907 (tt) REVERT: E 17 ARG cc_start: 0.6371 (ttt90) cc_final: 0.6063 (tpp80) REVERT: G 71 MET cc_start: 0.5604 (mpp) cc_final: 0.5286 (mmp) REVERT: H 3 ASN cc_start: 0.7177 (t0) cc_final: 0.6823 (m-40) REVERT: H 128 ASN cc_start: 0.6513 (p0) cc_final: 0.6064 (p0) REVERT: J 52 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7478 (p) REVERT: L 49 LYS cc_start: 0.8306 (mmpt) cc_final: 0.7413 (mttm) REVERT: N 57 LYS cc_start: 0.1919 (mmmt) cc_final: 0.1140 (ttpt) outliers start: 52 outliers final: 7 residues processed: 983 average time/residue: 0.2416 time to fit residues: 377.6041 Evaluate side-chains 503 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 491 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain M residue 52 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 0.0870 chunk 244 optimal weight: 20.0000 overall best weight: 2.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN A 795 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1191 GLN A1293 HIS A1314 GLN A1443 GLN A1599 ASN B 128 GLN B 282 HIS ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS B 427 GLN ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN B 735 HIS B 767 ASN B 770 ASN B 824 HIS B 896 GLN B1034 GLN B1038 HIS C 53 ASN C 99 HIS C 130 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** I 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN L 66 GLN N 85 HIS ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.190125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.168318 restraints weight = 62032.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.167684 restraints weight = 80343.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.168624 restraints weight = 66959.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.169123 restraints weight = 52143.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.169193 restraints weight = 45547.093| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 35340 Z= 0.191 Angle : 0.758 17.072 48078 Z= 0.377 Chirality : 0.047 0.243 5380 Planarity : 0.006 0.069 5924 Dihedral : 14.320 172.328 5407 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.72 % Favored : 93.16 % Rotamer: Outliers : 3.22 % Allowed : 15.87 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.11), residues: 4063 helix: -2.00 (0.12), residues: 1271 sheet: -2.38 (0.19), residues: 575 loop : -2.69 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 277 TYR 0.042 0.002 TYR A1573 PHE 0.021 0.002 PHE A1297 TRP 0.027 0.002 TRP H 79 HIS 0.012 0.002 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (35318) covalent geometry : angle 0.72888 / 0.37 (48051) hydrogen bonds : bond 0.04941 / 3.26 ( 1082) hydrogen bonds : angle 7.13625 / 4.88 ( 3115) metal coordination : bond 0.01757 / 1.15 ( 22) metal coordination : angle 8.84040 / 4.98 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 521 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.7589 (mp) cc_final: 0.7305 (mt) REVERT: A 348 LYS cc_start: 0.7384 (mmmt) cc_final: 0.7021 (mmmt) REVERT: A 458 GLN cc_start: 0.6231 (pm20) cc_final: 0.5858 (pm20) REVERT: A 618 TYR cc_start: 0.7346 (m-10) cc_final: 0.7013 (m-80) REVERT: A 1049 MET cc_start: 0.7573 (mtt) cc_final: 0.7205 (mmm) REVERT: A 1132 TYR cc_start: 0.3141 (m-10) cc_final: 0.2910 (m-10) REVERT: A 1172 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7681 (tp) REVERT: A 1294 MET cc_start: 0.5205 (mmt) cc_final: 0.3756 (ptm) REVERT: A 1456 PHE cc_start: 0.5306 (p90) cc_final: 0.3847 (m-80) REVERT: A 1457 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.5791 (mm) REVERT: A 1503 HIS cc_start: 0.6151 (m-70) cc_final: 0.5944 (m-70) REVERT: A 1519 LEU cc_start: 0.4294 (OUTLIER) cc_final: 0.4051 (tt) REVERT: A 1550 LEU cc_start: 0.7472 (tm) cc_final: 0.7191 (mt) REVERT: A 1553 TYR cc_start: 0.8231 (m-80) cc_final: 0.8013 (m-80) REVERT: A 1588 MET cc_start: 0.7725 (tpt) cc_final: 0.7516 (tpt) REVERT: A 1617 THR cc_start: 0.7362 (OUTLIER) cc_final: 0.7026 (p) REVERT: B 243 GLN cc_start: 0.4061 (pp30) cc_final: 0.3830 (pp30) REVERT: B 407 PHE cc_start: 0.6172 (OUTLIER) cc_final: 0.5522 (m-10) REVERT: B 436 MET cc_start: 0.3651 (ptp) cc_final: 0.3447 (pmm) REVERT: B 690 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6719 (tt0) REVERT: B 858 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6750 (tt) REVERT: B 977 ILE cc_start: 0.7655 (tt) cc_final: 0.7048 (tp) REVERT: B 1007 TYR cc_start: 0.8038 (t80) cc_final: 0.7757 (t80) REVERT: B 1039 MET cc_start: 0.7443 (tmt) cc_final: 0.6629 (tmt) REVERT: B 1074 MET cc_start: 0.7601 (mmt) cc_final: 0.7309 (mmm) REVERT: B 1133 MET cc_start: 0.6105 (tpp) cc_final: 0.5778 (tpt) REVERT: C 274 THR cc_start: 0.5112 (OUTLIER) cc_final: 0.4349 (t) REVERT: E 192 ARG cc_start: 0.7309 (mtt90) cc_final: 0.6568 (ptp-110) REVERT: F 85 MET cc_start: 0.7756 (tpp) cc_final: 0.6892 (tpp) REVERT: G 71 MET cc_start: 0.5710 (mpp) cc_final: 0.5423 (mmp) REVERT: G 126 GLN cc_start: 0.5056 (OUTLIER) cc_final: 0.3278 (mp10) REVERT: H 128 ASN cc_start: 0.6298 (p0) cc_final: 0.5952 (p0) REVERT: J 52 THR cc_start: 0.7758 (m) cc_final: 0.7420 (p) REVERT: J 67 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6287 (mt-10) REVERT: L 49 LYS cc_start: 0.8364 (mmpt) cc_final: 0.7434 (mttt) REVERT: N 57 LYS cc_start: 0.2286 (mmmt) cc_final: 0.1412 (ttpt) REVERT: N 169 GLU cc_start: 0.3934 (tm-30) cc_final: 0.3588 (tm-30) outliers start: 118 outliers final: 54 residues processed: 617 average time/residue: 0.2241 time to fit residues: 228.5705 Evaluate side-chains 485 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 423 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1237 GLN Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1609 SER Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 148 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 343 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 373 optimal weight: 2.9990 chunk 331 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 367 optimal weight: 5.9990 chunk 179 optimal weight: 0.3980 chunk 308 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.186504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.164739 restraints weight = 62072.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.164167 restraints weight = 84634.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.165531 restraints weight = 70739.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.165661 restraints weight = 50432.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.165788 restraints weight = 46232.517| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35340 Z= 0.172 Angle : 0.696 17.111 48078 Z= 0.350 Chirality : 0.046 0.279 5380 Planarity : 0.005 0.064 5924 Dihedral : 14.411 170.148 5398 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.46 % Favored : 92.42 % Rotamer: Outliers : 4.55 % Allowed : 15.82 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.12), residues: 4063 helix: -1.44 (0.13), residues: 1287 sheet: -2.09 (0.20), residues: 579 loop : -2.51 (0.12), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 7 TYR 0.027 0.002 TYR A1302 PHE 0.029 0.002 PHE A1297 TRP 0.024 0.002 TRP B 143 HIS 0.011 0.001 HIS B 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (35318) covalent geometry : angle 0.67708 / 0.35 (48051) hydrogen bonds : bond 0.04506 / 2.96 ( 1082) hydrogen bonds : angle 6.56988 / 4.51 ( 3115) metal coordination : bond 0.01316 / 0.91 ( 22) metal coordination : angle 6.80191 / 4.08 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 469 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5828 (mp) REVERT: A 348 LYS cc_start: 0.7457 (mmmt) cc_final: 0.7044 (mmmt) REVERT: A 470 HIS cc_start: 0.7887 (m-70) cc_final: 0.7580 (m170) REVERT: A 600 MET cc_start: 0.7058 (ttt) cc_final: 0.6793 (ttt) REVERT: A 618 TYR cc_start: 0.7424 (m-10) cc_final: 0.7096 (m-80) REVERT: A 846 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7529 (mp) REVERT: A 905 SER cc_start: 0.7314 (p) cc_final: 0.7056 (t) REVERT: A 1049 MET cc_start: 0.7687 (mtt) cc_final: 0.7193 (mmm) REVERT: A 1172 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7727 (tp) REVERT: A 1227 MET cc_start: 0.5940 (mtt) cc_final: 0.5415 (mmm) REVERT: A 1294 MET cc_start: 0.5680 (mmt) cc_final: 0.4020 (ptm) REVERT: A 1457 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6224 (mt) REVERT: A 1553 TYR cc_start: 0.8289 (m-80) cc_final: 0.8069 (m-80) REVERT: A 1613 MET cc_start: 0.6509 (mtp) cc_final: 0.6087 (mtt) REVERT: B 45 HIS cc_start: 0.6124 (m90) cc_final: 0.5380 (m170) REVERT: B 270 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7014 (mp) REVERT: B 407 PHE cc_start: 0.6337 (OUTLIER) cc_final: 0.5736 (m-10) REVERT: B 690 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6687 (tt0) REVERT: B 858 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6662 (tt) REVERT: B 1007 TYR cc_start: 0.8279 (t80) cc_final: 0.7919 (t80) REVERT: B 1039 MET cc_start: 0.7597 (tmt) cc_final: 0.6850 (tmt) REVERT: B 1133 MET cc_start: 0.6199 (tpp) cc_final: 0.5721 (tpt) REVERT: C 92 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6525 (mt) REVERT: C 293 ARG cc_start: 0.6964 (mpt180) cc_final: 0.6715 (mpt180) REVERT: E 192 ARG cc_start: 0.7253 (mtt90) cc_final: 0.6959 (ptp-110) REVERT: F 85 MET cc_start: 0.7823 (tpp) cc_final: 0.7034 (tpp) REVERT: F 122 MET cc_start: 0.6232 (mtp) cc_final: 0.5993 (mtm) REVERT: G 71 MET cc_start: 0.6140 (mpp) cc_final: 0.5700 (mmp) REVERT: G 126 GLN cc_start: 0.5120 (OUTLIER) cc_final: 0.4038 (pp30) REVERT: H 11 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7627 (tm-30) REVERT: H 128 ASN cc_start: 0.6555 (p0) cc_final: 0.6167 (p0) REVERT: J 49 MET cc_start: 0.8302 (mmm) cc_final: 0.7633 (mmm) REVERT: J 52 THR cc_start: 0.7952 (m) cc_final: 0.7631 (p) REVERT: K 110 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.5950 (pt0) REVERT: L 49 LYS cc_start: 0.8351 (mmpt) cc_final: 0.7578 (mttt) REVERT: L 66 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7955 (tm-30) REVERT: N 57 LYS cc_start: 0.2354 (mmmt) cc_final: 0.1289 (ttpp) REVERT: N 62 VAL cc_start: 0.3638 (OUTLIER) cc_final: 0.3425 (t) REVERT: N 107 MET cc_start: 0.5844 (mmm) cc_final: 0.4890 (pmm) outliers start: 167 outliers final: 95 residues processed: 595 average time/residue: 0.2155 time to fit residues: 212.9491 Evaluate side-chains 520 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 414 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1237 GLN Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1609 SER Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 148 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 183 optimal weight: 1.9990 chunk 275 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 282 optimal weight: 0.4980 chunk 290 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 245 optimal weight: 0.6980 chunk 402 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 216 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 282 HIS ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN I 19 ASN I 32 GLN ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.184741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.160750 restraints weight = 61900.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.160644 restraints weight = 77594.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.161546 restraints weight = 67725.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.162206 restraints weight = 50626.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.162299 restraints weight = 41992.246| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35340 Z= 0.157 Angle : 0.683 16.011 48078 Z= 0.342 Chirality : 0.045 0.278 5380 Planarity : 0.005 0.063 5924 Dihedral : 14.471 168.504 5398 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.78 % Favored : 92.10 % Rotamer: Outliers : 4.80 % Allowed : 16.61 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.12), residues: 4063 helix: -1.09 (0.14), residues: 1284 sheet: -1.90 (0.20), residues: 589 loop : -2.37 (0.12), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 305 TYR 0.026 0.002 TYR H 116 PHE 0.023 0.002 PHE C 315 TRP 0.025 0.002 TRP B 143 HIS 0.019 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (35318) covalent geometry : angle 0.66970 / 0.34 (48051) hydrogen bonds : bond 0.04149 / 2.76 ( 1082) hydrogen bonds : angle 6.16482 / 4.24 ( 3115) metal coordination : bond 0.01036 / 0.66 ( 22) metal coordination : angle 5.79595 / 3.53 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 453 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8182 (mm) cc_final: 0.7469 (mm) REVERT: A 324 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5834 (mp) REVERT: A 618 TYR cc_start: 0.7427 (m-10) cc_final: 0.7169 (m-80) REVERT: A 810 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7245 (mt) REVERT: A 830 MET cc_start: 0.8466 (tpt) cc_final: 0.8123 (tpt) REVERT: A 905 SER cc_start: 0.7471 (p) cc_final: 0.7208 (t) REVERT: A 1049 MET cc_start: 0.7690 (mtt) cc_final: 0.7225 (mmm) REVERT: A 1170 MET cc_start: 0.7025 (tpt) cc_final: 0.6728 (tpp) REVERT: A 1172 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7707 (tp) REVERT: A 1227 MET cc_start: 0.6236 (mtt) cc_final: 0.5782 (mmm) REVERT: A 1457 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6143 (mt) REVERT: A 1613 MET cc_start: 0.6535 (mtp) cc_final: 0.6166 (mtt) REVERT: A 1617 THR cc_start: 0.7546 (OUTLIER) cc_final: 0.6998 (p) REVERT: B 45 HIS cc_start: 0.5896 (m90) cc_final: 0.5576 (m170) REVERT: B 243 GLN cc_start: 0.4636 (pp30) cc_final: 0.4099 (pp30) REVERT: B 270 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.6956 (mp) REVERT: B 407 PHE cc_start: 0.6714 (OUTLIER) cc_final: 0.5632 (m-10) REVERT: B 411 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.6502 (mpp) REVERT: B 502 MET cc_start: 0.7583 (ttm) cc_final: 0.7164 (ttm) REVERT: B 690 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6548 (tt0) REVERT: B 1039 MET cc_start: 0.7773 (tmt) cc_final: 0.7000 (tmt) REVERT: B 1111 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6345 (mt) REVERT: B 1133 MET cc_start: 0.6149 (tpp) cc_final: 0.5758 (tpt) REVERT: C 92 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6539 (mt) REVERT: C 218 LYS cc_start: 0.6968 (pttt) cc_final: 0.5956 (mtmt) REVERT: C 293 ARG cc_start: 0.7158 (mpt180) cc_final: 0.6838 (mpt180) REVERT: D 44 ILE cc_start: 0.2110 (OUTLIER) cc_final: 0.1776 (mm) REVERT: F 65 ARG cc_start: 0.4668 (ppt170) cc_final: 0.4337 (ppt170) REVERT: F 108 PHE cc_start: 0.5744 (m-80) cc_final: 0.5503 (m-80) REVERT: F 122 MET cc_start: 0.6504 (mtp) cc_final: 0.6209 (mtm) REVERT: G 126 GLN cc_start: 0.5287 (OUTLIER) cc_final: 0.4127 (pp30) REVERT: H 11 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7625 (tm-30) REVERT: H 123 MET cc_start: 0.3894 (mtp) cc_final: 0.3665 (mtt) REVERT: H 128 ASN cc_start: 0.6631 (p0) cc_final: 0.6206 (p0) REVERT: J 52 THR cc_start: 0.8113 (m) cc_final: 0.7853 (p) REVERT: K 110 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6000 (pt0) REVERT: L 49 LYS cc_start: 0.8189 (mmpt) cc_final: 0.7547 (mtmt) REVERT: N 57 LYS cc_start: 0.2597 (mmmt) cc_final: 0.1832 (ttpt) outliers start: 176 outliers final: 107 residues processed: 587 average time/residue: 0.2099 time to fit residues: 206.8180 Evaluate side-chains 507 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 387 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 148 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 6 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 287 optimal weight: 8.9990 chunk 387 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 chunk 318 optimal weight: 6.9990 chunk 225 optimal weight: 0.8980 chunk 285 optimal weight: 8.9990 chunk 67 optimal weight: 0.0040 chunk 55 optimal weight: 0.8980 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN E 99 HIS K 64 GLN ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.186411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.162293 restraints weight = 61479.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.162300 restraints weight = 79588.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.163521 restraints weight = 66758.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.164042 restraints weight = 47731.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.164183 restraints weight = 40874.938| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 35340 Z= 0.129 Angle : 0.668 13.782 48078 Z= 0.333 Chirality : 0.045 0.282 5380 Planarity : 0.005 0.063 5924 Dihedral : 14.479 167.318 5398 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.21 % Favored : 92.67 % Rotamer: Outliers : 4.09 % Allowed : 18.30 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.12), residues: 4063 helix: -0.87 (0.14), residues: 1286 sheet: -1.77 (0.20), residues: 587 loop : -2.25 (0.12), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 379 TYR 0.028 0.002 TYR A1302 PHE 0.021 0.001 PHE J 8 TRP 0.042 0.002 TRP E 13 HIS 0.019 0.001 HIS B 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (35318) covalent geometry : angle 0.65730 / 0.33 (48051) hydrogen bonds : bond 0.03943 / 2.62 ( 1082) hydrogen bonds : angle 5.92019 / 4.06 ( 3115) metal coordination : bond 0.00870 / 0.58 ( 22) metal coordination : angle 5.16763 / 3.05 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 435 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8085 (mm) cc_final: 0.7820 (mm) REVERT: A 470 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7469 (m170) REVERT: A 618 TYR cc_start: 0.7253 (m-10) cc_final: 0.7033 (m-80) REVERT: A 642 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7317 (t0) REVERT: A 810 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7166 (mt) REVERT: A 846 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7516 (mp) REVERT: A 905 SER cc_start: 0.7609 (p) cc_final: 0.7366 (t) REVERT: A 1049 MET cc_start: 0.7678 (mtt) cc_final: 0.7198 (mmm) REVERT: A 1170 MET cc_start: 0.6922 (tpt) cc_final: 0.6715 (tpp) REVERT: A 1172 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7648 (tp) REVERT: A 1178 LEU cc_start: 0.7674 (mm) cc_final: 0.7274 (mm) REVERT: A 1457 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.5876 (mt) REVERT: A 1617 THR cc_start: 0.7404 (OUTLIER) cc_final: 0.6839 (p) REVERT: A 1654 PHE cc_start: 0.8533 (p90) cc_final: 0.8299 (p90) REVERT: B 45 HIS cc_start: 0.5854 (m90) cc_final: 0.5462 (m170) REVERT: B 270 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7350 (mt) REVERT: B 502 MET cc_start: 0.7556 (ttm) cc_final: 0.7123 (ttm) REVERT: B 568 LEU cc_start: 0.4939 (mt) cc_final: 0.4617 (mt) REVERT: B 690 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6608 (tt0) REVERT: B 1007 TYR cc_start: 0.8350 (t80) cc_final: 0.7940 (t80) REVERT: B 1039 MET cc_start: 0.7646 (tmt) cc_final: 0.6951 (tmt) REVERT: B 1111 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6426 (mt) REVERT: B 1133 MET cc_start: 0.6132 (tpp) cc_final: 0.5688 (tpt) REVERT: C 47 LEU cc_start: 0.5269 (OUTLIER) cc_final: 0.4803 (tp) REVERT: C 218 LYS cc_start: 0.6879 (pttt) cc_final: 0.6333 (tptp) REVERT: C 293 ARG cc_start: 0.7014 (mpt180) cc_final: 0.6558 (mpt180) REVERT: D 44 ILE cc_start: 0.1984 (OUTLIER) cc_final: 0.1666 (mm) REVERT: F 100 GLN cc_start: 0.7163 (mt0) cc_final: 0.6926 (mt0) REVERT: G 126 GLN cc_start: 0.5309 (OUTLIER) cc_final: 0.4106 (pp30) REVERT: H 11 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7715 (tm-30) REVERT: H 128 ASN cc_start: 0.6391 (p0) cc_final: 0.6107 (p0) REVERT: J 52 THR cc_start: 0.8061 (m) cc_final: 0.7753 (p) REVERT: K 110 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.5918 (pt0) REVERT: L 49 LYS cc_start: 0.8127 (mmpt) cc_final: 0.7526 (mttt) REVERT: M 31 ARG cc_start: 0.3315 (OUTLIER) cc_final: 0.2598 (ptp-170) REVERT: N 57 LYS cc_start: 0.2573 (mmmt) cc_final: 0.1806 (ttpt) REVERT: N 107 MET cc_start: 0.5204 (mmm) cc_final: 0.4638 (pmm) outliers start: 150 outliers final: 90 residues processed: 549 average time/residue: 0.2122 time to fit residues: 195.6801 Evaluate side-chains 505 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 401 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1079 LYS Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 142 MET Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 148 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 347 optimal weight: 10.0000 chunk 345 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 348 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 265 optimal weight: 4.9990 chunk 258 optimal weight: 0.3980 chunk 398 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1567 ASN B 128 GLN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 243 GLN B 282 HIS ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS B 499 HIS ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.181335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.158806 restraints weight = 61764.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.158514 restraints weight = 95347.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.159743 restraints weight = 76803.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.159936 restraints weight = 58399.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.160079 restraints weight = 49684.235| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35340 Z= 0.185 Angle : 0.708 14.960 48078 Z= 0.356 Chirality : 0.046 0.278 5380 Planarity : 0.005 0.061 5924 Dihedral : 14.558 167.477 5397 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.81 % Favored : 91.09 % Rotamer: Outliers : 5.04 % Allowed : 18.13 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.13), residues: 4063 helix: -0.76 (0.14), residues: 1284 sheet: -1.70 (0.20), residues: 584 loop : -2.25 (0.12), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 127 TYR 0.024 0.002 TYR A1302 PHE 0.019 0.002 PHE A 771 TRP 0.060 0.002 TRP E 13 HIS 0.009 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (35318) covalent geometry : angle 0.69805 / 0.36 (48051) hydrogen bonds : bond 0.04090 / 2.73 ( 1082) hydrogen bonds : angle 5.89102 / 4.06 ( 3115) metal coordination : bond 0.00937 / 0.60 ( 22) metal coordination : angle 5.00702 / 3.11 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 422 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8245 (mm) cc_final: 0.7929 (mm) REVERT: A 324 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6016 (mp) REVERT: A 462 LYS cc_start: -0.3671 (OUTLIER) cc_final: -0.4294 (pttm) REVERT: A 553 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.5438 (mm-40) REVERT: A 618 TYR cc_start: 0.7499 (m-10) cc_final: 0.7232 (m-80) REVERT: A 633 MET cc_start: 0.7633 (ptp) cc_final: 0.7337 (mtm) REVERT: A 846 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7513 (mp) REVERT: A 905 SER cc_start: 0.7433 (p) cc_final: 0.7165 (t) REVERT: A 1049 MET cc_start: 0.7774 (mtt) cc_final: 0.7216 (mmm) REVERT: A 1170 MET cc_start: 0.7207 (tpt) cc_final: 0.6854 (tpp) REVERT: A 1172 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7800 (tp) REVERT: A 1178 LEU cc_start: 0.7715 (mm) cc_final: 0.7367 (mm) REVERT: A 1227 MET cc_start: 0.6277 (mtt) cc_final: 0.5721 (mmm) REVERT: A 1457 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.5902 (mt) REVERT: A 1617 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7165 (p) REVERT: B 243 GLN cc_start: 0.4978 (OUTLIER) cc_final: 0.4678 (pp30) REVERT: B 270 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7435 (mt) REVERT: B 407 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.5773 (m-10) REVERT: B 502 MET cc_start: 0.7687 (ttm) cc_final: 0.7251 (ttm) REVERT: B 541 LEU cc_start: 0.8135 (mt) cc_final: 0.7820 (mp) REVERT: B 690 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6660 (tt0) REVERT: B 721 MET cc_start: 0.6353 (mmp) cc_final: 0.6063 (mmp) REVERT: B 1111 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5114 (pp) REVERT: B 1133 MET cc_start: 0.6372 (tpp) cc_final: 0.6007 (tpt) REVERT: C 47 LEU cc_start: 0.5215 (OUTLIER) cc_final: 0.4807 (tp) REVERT: C 71 MET cc_start: 0.6035 (mmt) cc_final: 0.5773 (mmt) REVERT: C 92 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6533 (mt) REVERT: C 94 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6426 (t0) REVERT: C 218 LYS cc_start: 0.6784 (pttt) cc_final: 0.6171 (tptm) REVERT: C 293 ARG cc_start: 0.7035 (mpt180) cc_final: 0.6763 (mpt180) REVERT: D 44 ILE cc_start: 0.2179 (OUTLIER) cc_final: 0.1862 (mm) REVERT: E 13 TRP cc_start: 0.4625 (t60) cc_final: 0.4361 (t60) REVERT: E 25 ASP cc_start: 0.7128 (p0) cc_final: 0.6783 (p0) REVERT: F 100 GLN cc_start: 0.7294 (mt0) cc_final: 0.7081 (mt0) REVERT: G 121 ASN cc_start: 0.7613 (m-40) cc_final: 0.6330 (p0) REVERT: G 126 GLN cc_start: 0.5502 (OUTLIER) cc_final: 0.4351 (pp30) REVERT: H 11 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7764 (tm-30) REVERT: H 128 ASN cc_start: 0.6693 (p0) cc_final: 0.6425 (p0) REVERT: J 52 THR cc_start: 0.7896 (m) cc_final: 0.7626 (p) REVERT: K 110 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6172 (pt0) REVERT: L 49 LYS cc_start: 0.8115 (mmpt) cc_final: 0.7560 (mtmt) REVERT: L 66 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8028 (tm-30) REVERT: M 31 ARG cc_start: 0.3564 (OUTLIER) cc_final: 0.2689 (ptp-170) REVERT: N 107 MET cc_start: 0.5294 (mmm) cc_final: 0.3864 (pmm) outliers start: 185 outliers final: 116 residues processed: 565 average time/residue: 0.2089 time to fit residues: 198.1546 Evaluate side-chains 521 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 387 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1079 LYS Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 142 MET Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 148 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 207 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 319 optimal weight: 2.9990 chunk 371 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 403 optimal weight: 30.0000 chunk 157 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN K 70 HIS K 106 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.175250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.155987 restraints weight = 63131.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.155211 restraints weight = 89026.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.155915 restraints weight = 82433.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.155454 restraints weight = 65736.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.155764 restraints weight = 57219.608| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 35340 Z= 0.269 Angle : 0.821 20.314 48078 Z= 0.419 Chirality : 0.050 0.294 5380 Planarity : 0.006 0.066 5924 Dihedral : 14.804 167.479 5397 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.92 % Favored : 89.98 % Rotamer: Outliers : 5.32 % Allowed : 18.41 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.12), residues: 4063 helix: -0.96 (0.14), residues: 1285 sheet: -1.82 (0.21), residues: 580 loop : -2.40 (0.12), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 127 TYR 0.032 0.003 TYR H 116 PHE 0.035 0.003 PHE J 8 TRP 0.040 0.003 TRP E 13 HIS 0.012 0.002 HIS B 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.27 (35318) covalent geometry : angle 0.81172 / 0.42 (48051) hydrogen bonds : bond 0.04774 / 3.17 ( 1082) hydrogen bonds : angle 6.16314 / 4.24 ( 3115) metal coordination : bond 0.01318 / 0.78 ( 22) metal coordination : angle 5.38662 / 3.46 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 410 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 324 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5900 (mp) REVERT: A 462 LYS cc_start: -0.3344 (OUTLIER) cc_final: -0.4181 (pttm) REVERT: A 553 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.5117 (mm-40) REVERT: A 633 MET cc_start: 0.7542 (ptp) cc_final: 0.7139 (mtm) REVERT: A 683 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6015 (ptmt) REVERT: A 692 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.6220 (t80) REVERT: A 830 MET cc_start: 0.8655 (tpt) cc_final: 0.8355 (tpt) REVERT: A 846 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7549 (mp) REVERT: A 905 SER cc_start: 0.7244 (p) cc_final: 0.6969 (t) REVERT: A 1034 TYR cc_start: 0.6500 (m-80) cc_final: 0.5676 (m-80) REVERT: A 1172 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8118 (tp) REVERT: A 1178 LEU cc_start: 0.7776 (mm) cc_final: 0.7483 (mm) REVERT: A 1237 GLN cc_start: 0.6557 (OUTLIER) cc_final: 0.6312 (tt0) REVERT: A 1457 ILE cc_start: 0.6932 (OUTLIER) cc_final: 0.5947 (mt) REVERT: A 1617 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7596 (p) REVERT: B 270 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.6984 (pt) REVERT: B 407 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6314 (m-10) REVERT: B 496 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.5635 (t80) REVERT: B 502 MET cc_start: 0.7724 (ttm) cc_final: 0.7311 (ttm) REVERT: B 541 LEU cc_start: 0.8236 (mt) cc_final: 0.7947 (mp) REVERT: B 745 GLN cc_start: 0.7546 (mt0) cc_final: 0.7313 (mt0) REVERT: B 840 LEU cc_start: 0.4698 (tp) cc_final: 0.4482 (tp) REVERT: B 1111 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.4941 (pp) REVERT: B 1133 MET cc_start: 0.6352 (tpp) cc_final: 0.6056 (tpt) REVERT: C 71 MET cc_start: 0.6097 (mmt) cc_final: 0.5857 (mmt) REVERT: C 92 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6328 (mt) REVERT: C 94 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6653 (t0) REVERT: C 293 ARG cc_start: 0.7302 (mpt180) cc_final: 0.7076 (mpt180) REVERT: D 44 ILE cc_start: 0.1956 (OUTLIER) cc_final: 0.1623 (mm) REVERT: E 13 TRP cc_start: 0.7044 (t60) cc_final: 0.5756 (t60) REVERT: E 58 MET cc_start: 0.5906 (tmm) cc_final: 0.5557 (ttp) REVERT: F 108 PHE cc_start: 0.6145 (m-80) cc_final: 0.5867 (m-80) REVERT: G 71 MET cc_start: 0.6499 (mmp) cc_final: 0.6291 (mmm) REVERT: G 88 LYS cc_start: 0.7362 (tmtt) cc_final: 0.7136 (tttm) REVERT: G 121 ASN cc_start: 0.7629 (m-40) cc_final: 0.6278 (p0) REVERT: G 126 GLN cc_start: 0.5399 (OUTLIER) cc_final: 0.4212 (pp30) REVERT: H 11 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7775 (tm-30) REVERT: H 128 ASN cc_start: 0.6712 (p0) cc_final: 0.6472 (p0) REVERT: K 110 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6188 (pt0) REVERT: L 49 LYS cc_start: 0.8372 (mmpt) cc_final: 0.7878 (mtmt) REVERT: M 31 ARG cc_start: 0.3739 (OUTLIER) cc_final: 0.2988 (ptp-170) outliers start: 195 outliers final: 134 residues processed: 562 average time/residue: 0.2000 time to fit residues: 188.9657 Evaluate side-chains 505 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 351 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 683 LYS Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1079 LYS Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1237 GLN Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1293 HIS Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1576 SER Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1623 THR Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 148 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 125 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 406 optimal weight: 0.0970 chunk 329 optimal weight: 20.0000 chunk 291 optimal weight: 9.9990 chunk 306 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 380 optimal weight: 1.9990 chunk 311 optimal weight: 0.7980 chunk 270 optimal weight: 0.0170 chunk 199 optimal weight: 4.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.181248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.156798 restraints weight = 61909.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.156532 restraints weight = 78300.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.157354 restraints weight = 66450.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.157784 restraints weight = 57948.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.158043 restraints weight = 48179.096| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 35340 Z= 0.139 Angle : 0.714 15.770 48078 Z= 0.356 Chirality : 0.046 0.296 5380 Planarity : 0.005 0.098 5924 Dihedral : 14.689 167.057 5397 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.61 % Favored : 92.30 % Rotamer: Outliers : 3.38 % Allowed : 20.83 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.13), residues: 4063 helix: -0.53 (0.14), residues: 1271 sheet: -1.61 (0.21), residues: 574 loop : -2.19 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 92 TYR 0.046 0.002 TYR A 618 PHE 0.028 0.002 PHE J 8 TRP 0.029 0.002 TRP E 13 HIS 0.022 0.001 HIS B 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (35318) covalent geometry : angle 0.70724 / 0.36 (48051) hydrogen bonds : bond 0.03916 / 2.61 ( 1082) hydrogen bonds : angle 5.74294 / 3.95 ( 3115) metal coordination : bond 0.00699 / 0.46 ( 22) metal coordination : angle 4.23505 / 2.62 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 423 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7154 (mm-30) REVERT: A 238 MET cc_start: 0.5655 (pmm) cc_final: 0.4719 (tpt) REVERT: A 462 LYS cc_start: -0.3886 (OUTLIER) cc_final: -0.4402 (pttm) REVERT: A 470 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.6975 (m170) REVERT: A 553 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.5495 (mm-40) REVERT: A 633 MET cc_start: 0.7598 (ptp) cc_final: 0.7204 (mtm) REVERT: A 635 MET cc_start: 0.8243 (tmm) cc_final: 0.7967 (tmm) REVERT: A 830 MET cc_start: 0.8490 (tpt) cc_final: 0.8270 (tpt) REVERT: A 905 SER cc_start: 0.7379 (p) cc_final: 0.7150 (t) REVERT: A 1034 TYR cc_start: 0.5980 (m-80) cc_final: 0.5367 (m-80) REVERT: A 1178 LEU cc_start: 0.7590 (mm) cc_final: 0.7271 (mm) REVERT: A 1457 ILE cc_start: 0.6906 (OUTLIER) cc_final: 0.5986 (mt) REVERT: A 1617 THR cc_start: 0.7410 (OUTLIER) cc_final: 0.6792 (p) REVERT: B 270 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.6939 (pt) REVERT: B 407 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.5989 (m-10) REVERT: B 502 MET cc_start: 0.7568 (ttm) cc_final: 0.7277 (ttm) REVERT: B 690 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6576 (tt0) REVERT: B 1013 MET cc_start: 0.7210 (ttt) cc_final: 0.6960 (ttt) REVERT: B 1075 GLU cc_start: 0.7744 (tp30) cc_final: 0.7467 (tp30) REVERT: B 1111 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6823 (mt) REVERT: B 1133 MET cc_start: 0.5876 (tpp) cc_final: 0.5471 (tpt) REVERT: C 47 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.5078 (tp) REVERT: C 94 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6197 (t0) REVERT: C 120 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.5563 (tp) REVERT: C 218 LYS cc_start: 0.7164 (pttt) cc_final: 0.6651 (tptm) REVERT: C 235 ILE cc_start: 0.7644 (mm) cc_final: 0.7150 (mm) REVERT: C 293 ARG cc_start: 0.7341 (mpt180) cc_final: 0.7034 (mpt180) REVERT: D 44 ILE cc_start: 0.2239 (OUTLIER) cc_final: 0.1999 (mm) REVERT: E 13 TRP cc_start: 0.7469 (t60) cc_final: 0.6951 (t60) REVERT: E 58 MET cc_start: 0.5788 (tmm) cc_final: 0.5560 (ttp) REVERT: F 65 ARG cc_start: 0.4607 (ppt170) cc_final: 0.3682 (ttt180) REVERT: G 71 MET cc_start: 0.6350 (mmp) cc_final: 0.6035 (mmm) REVERT: G 118 CYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6485 (p) REVERT: G 126 GLN cc_start: 0.5429 (OUTLIER) cc_final: 0.4195 (pp30) REVERT: H 11 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7815 (tm-30) REVERT: H 24 CYS cc_start: 0.7882 (m) cc_final: 0.7441 (p) REVERT: H 128 ASN cc_start: 0.6211 (p0) cc_final: 0.5995 (p0) REVERT: K 110 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6256 (pt0) REVERT: L 49 LYS cc_start: 0.8274 (mmpt) cc_final: 0.7886 (mtmt) REVERT: M 31 ARG cc_start: 0.3621 (OUTLIER) cc_final: 0.2795 (ptp-170) outliers start: 124 outliers final: 81 residues processed: 519 average time/residue: 0.2088 time to fit residues: 181.0814 Evaluate side-chains 486 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 389 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1079 LYS Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 148 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 121 optimal weight: 10.0000 chunk 364 optimal weight: 7.9990 chunk 306 optimal weight: 10.0000 chunk 292 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 411 optimal weight: 50.0000 chunk 38 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 324 optimal weight: 0.0770 overall best weight: 3.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.176331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.156827 restraints weight = 62569.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.155919 restraints weight = 107990.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.156802 restraints weight = 93983.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.156925 restraints weight = 66688.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.157122 restraints weight = 58144.201| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 35340 Z= 0.226 Angle : 0.780 17.049 48078 Z= 0.397 Chirality : 0.049 0.360 5380 Planarity : 0.006 0.084 5924 Dihedral : 14.785 165.631 5397 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.60 % Favored : 90.30 % Rotamer: Outliers : 3.49 % Allowed : 21.00 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.13), residues: 4063 helix: -0.63 (0.14), residues: 1279 sheet: -1.72 (0.21), residues: 553 loop : -2.24 (0.12), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1517 TYR 0.079 0.003 TYR A 618 PHE 0.021 0.002 PHE C 36 TRP 0.034 0.003 TRP A 530 HIS 0.048 0.002 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (35318) covalent geometry : angle 0.77250 / 0.40 (48051) hydrogen bonds : bond 0.04392 / 2.96 ( 1082) hydrogen bonds : angle 5.94927 / 4.09 ( 3115) metal coordination : bond 0.01006 / 0.61 ( 22) metal coordination : angle 4.55008 / 2.96 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 388 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6990 (mm-30) REVERT: A 348 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7509 (mmmm) REVERT: A 462 LYS cc_start: -0.3565 (OUTLIER) cc_final: -0.4350 (pttm) REVERT: A 553 GLN cc_start: 0.6508 (OUTLIER) cc_final: 0.5346 (mm-40) REVERT: A 633 MET cc_start: 0.7542 (ptp) cc_final: 0.7267 (mtm) REVERT: A 635 MET cc_start: 0.7937 (tmm) cc_final: 0.7719 (tmm) REVERT: A 1178 LEU cc_start: 0.7515 (mm) cc_final: 0.7197 (mm) REVERT: A 1457 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.5893 (mt) REVERT: A 1617 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7243 (p) REVERT: B 270 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7059 (pt) REVERT: B 308 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8061 (mm) REVERT: B 407 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.6146 (m-10) REVERT: B 436 MET cc_start: 0.4168 (ptp) cc_final: 0.3893 (ptp) REVERT: B 476 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.5918 (pp) REVERT: B 502 MET cc_start: 0.7632 (ttm) cc_final: 0.7218 (ttm) REVERT: B 649 MET cc_start: 0.5589 (tpp) cc_final: 0.5199 (mmt) REVERT: B 745 GLN cc_start: 0.7468 (mt0) cc_final: 0.7261 (mt0) REVERT: B 1111 LEU cc_start: 0.6015 (OUTLIER) cc_final: 0.4990 (pp) REVERT: C 94 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6637 (t0) REVERT: C 120 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5827 (tp) REVERT: C 218 LYS cc_start: 0.7105 (pttt) cc_final: 0.6635 (tptm) REVERT: C 235 ILE cc_start: 0.7482 (mm) cc_final: 0.7101 (mm) REVERT: C 293 ARG cc_start: 0.7347 (mpt180) cc_final: 0.7076 (mpt180) REVERT: D 44 ILE cc_start: 0.2656 (OUTLIER) cc_final: 0.2326 (mm) REVERT: E 13 TRP cc_start: 0.7207 (t60) cc_final: 0.6895 (t60) REVERT: E 22 MET cc_start: 0.7981 (ppp) cc_final: 0.6302 (ppp) REVERT: F 65 ARG cc_start: 0.4790 (ppt170) cc_final: 0.3895 (ttt180) REVERT: G 71 MET cc_start: 0.6501 (mmp) cc_final: 0.6280 (mmm) REVERT: G 88 LYS cc_start: 0.7280 (tmtt) cc_final: 0.7068 (tttm) REVERT: G 118 CYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6725 (p) REVERT: G 126 GLN cc_start: 0.5260 (OUTLIER) cc_final: 0.4012 (pp30) REVERT: H 11 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7778 (tm-30) REVERT: H 128 ASN cc_start: 0.6314 (p0) cc_final: 0.6099 (p0) REVERT: K 110 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6240 (pt0) REVERT: L 49 LYS cc_start: 0.8280 (mmpt) cc_final: 0.7863 (mtmt) REVERT: M 31 ARG cc_start: 0.3703 (OUTLIER) cc_final: 0.2924 (ptp-170) outliers start: 128 outliers final: 96 residues processed: 489 average time/residue: 0.1971 time to fit residues: 162.2762 Evaluate side-chains 484 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 372 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1079 LYS Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 148 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 180 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 108 optimal weight: 0.2980 chunk 49 optimal weight: 0.4980 chunk 251 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 196 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 362 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1500 GLN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.181674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.157519 restraints weight = 61894.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.157639 restraints weight = 80520.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.159381 restraints weight = 62049.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.159195 restraints weight = 43727.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.159426 restraints weight = 40237.936| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35340 Z= 0.135 Angle : 0.720 17.979 48078 Z= 0.361 Chirality : 0.046 0.304 5380 Planarity : 0.005 0.090 5924 Dihedral : 14.710 167.560 5397 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.51 % Favored : 92.39 % Rotamer: Outliers : 2.84 % Allowed : 22.06 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.13), residues: 4063 helix: -0.45 (0.14), residues: 1280 sheet: -1.61 (0.21), residues: 571 loop : -2.06 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.053 0.002 TYR A 618 PHE 0.058 0.002 PHE E 82 TRP 0.039 0.002 TRP A 530 HIS 0.015 0.001 HIS B 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (35318) covalent geometry : angle 0.71577 / 0.36 (48051) hydrogen bonds : bond 0.03819 / 2.55 ( 1082) hydrogen bonds : angle 5.60855 / 3.86 ( 3115) metal coordination : bond 0.00605 / 0.39 ( 22) metal coordination : angle 3.49701 / 2.21 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 413 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7613 (ptm-80) cc_final: 0.7163 (ptp-170) REVERT: A 180 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7039 (mm-30) REVERT: A 238 MET cc_start: 0.5537 (pmm) cc_final: 0.4582 (tpt) REVERT: A 462 LYS cc_start: -0.3827 (OUTLIER) cc_final: -0.4284 (pttm) REVERT: A 509 GLU cc_start: 0.6407 (mm-30) cc_final: 0.6206 (mm-30) REVERT: A 549 MET cc_start: 0.4837 (tpp) cc_final: 0.4614 (tpp) REVERT: A 553 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.5256 (mm-40) REVERT: A 618 TYR cc_start: 0.7558 (m-80) cc_final: 0.7156 (m-80) REVERT: A 633 MET cc_start: 0.7788 (ptp) cc_final: 0.7380 (mtm) REVERT: A 635 MET cc_start: 0.8193 (tmm) cc_final: 0.7924 (tmm) REVERT: A 1034 TYR cc_start: 0.5998 (m-80) cc_final: 0.5425 (m-80) REVERT: A 1170 MET cc_start: 0.7026 (tpt) cc_final: 0.6802 (tpp) REVERT: A 1457 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.5949 (mt) REVERT: A 1617 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.6866 (p) REVERT: B 243 GLN cc_start: 0.4929 (pp30) cc_final: 0.4302 (pp30) REVERT: B 270 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7050 (pt) REVERT: B 407 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.6096 (m-10) REVERT: B 476 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5664 (pp) REVERT: B 502 MET cc_start: 0.7471 (ttm) cc_final: 0.7012 (ttm) REVERT: B 690 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6361 (tt0) REVERT: B 920 ARG cc_start: 0.8554 (ttm170) cc_final: 0.7957 (ttp-110) REVERT: B 1111 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6986 (mt) REVERT: C 94 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6310 (t0) REVERT: C 120 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5669 (tp) REVERT: C 218 LYS cc_start: 0.7014 (pttt) cc_final: 0.6511 (tptm) REVERT: C 235 ILE cc_start: 0.7613 (mm) cc_final: 0.7216 (mm) REVERT: C 293 ARG cc_start: 0.7327 (mpt180) cc_final: 0.7085 (mpt180) REVERT: D 44 ILE cc_start: 0.1947 (OUTLIER) cc_final: 0.1707 (mm) REVERT: E 13 TRP cc_start: 0.7264 (t60) cc_final: 0.7004 (t60) REVERT: E 22 MET cc_start: 0.7913 (ppp) cc_final: 0.6706 (ppp) REVERT: F 65 ARG cc_start: 0.4532 (ppt170) cc_final: 0.3761 (ttt180) REVERT: G 71 MET cc_start: 0.6445 (mmp) cc_final: 0.6179 (mmm) REVERT: G 88 LYS cc_start: 0.7241 (tmtt) cc_final: 0.7002 (tttm) REVERT: G 118 CYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6890 (p) REVERT: G 126 GLN cc_start: 0.5569 (OUTLIER) cc_final: 0.4133 (pp30) REVERT: H 11 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7803 (tm-30) REVERT: H 14 GLU cc_start: 0.6836 (tt0) cc_final: 0.6615 (tt0) REVERT: H 128 ASN cc_start: 0.6061 (p0) cc_final: 0.5843 (p0) REVERT: I 60 LEU cc_start: 0.4473 (OUTLIER) cc_final: 0.4012 (pt) REVERT: K 110 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6026 (pt0) REVERT: K 142 MET cc_start: 0.5633 (OUTLIER) cc_final: 0.5269 (mpp) REVERT: L 49 LYS cc_start: 0.8273 (mmpt) cc_final: 0.7902 (mtmt) REVERT: M 31 ARG cc_start: 0.3646 (OUTLIER) cc_final: 0.2829 (ptp-170) outliers start: 104 outliers final: 82 residues processed: 494 average time/residue: 0.1937 time to fit residues: 162.0876 Evaluate side-chains 485 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 386 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1079 LYS Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1535 PHE Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 142 MET Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 148 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 399 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 263 optimal weight: 0.6980 chunk 374 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 403 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.179967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.160015 restraints weight = 62097.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.159252 restraints weight = 97424.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.160160 restraints weight = 83427.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.160335 restraints weight = 59453.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.160429 restraints weight = 54311.546| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 35340 Z= 0.151 Angle : 0.721 17.503 48078 Z= 0.362 Chirality : 0.046 0.332 5380 Planarity : 0.005 0.087 5924 Dihedral : 14.693 166.593 5396 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.61 % Favored : 91.29 % Rotamer: Outliers : 2.95 % Allowed : 22.12 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.13), residues: 4063 helix: -0.38 (0.15), residues: 1280 sheet: -1.53 (0.21), residues: 564 loop : -2.06 (0.13), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.036 0.002 TYR A 618 PHE 0.030 0.002 PHE E 96 TRP 0.034 0.002 TRP A 530 HIS 0.010 0.001 HIS B 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (35318) covalent geometry : angle 0.71632 / 0.36 (48051) hydrogen bonds : bond 0.03846 / 2.55 ( 1082) hydrogen bonds : angle 5.59752 / 3.84 ( 3115) metal coordination : bond 0.00643 / 0.43 ( 22) metal coordination : angle 3.41545 / 2.25 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5441.85 seconds wall clock time: 95 minutes 48.55 seconds (5748.55 seconds total)