Starting phenix.real_space_refine on Thu Feb 22 15:08:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5x_3447/02_2024/5m5x_3447_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5x_3447/02_2024/5m5x_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5x_3447/02_2024/5m5x_3447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5x_3447/02_2024/5m5x_3447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5x_3447/02_2024/5m5x_3447_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5x_3447/02_2024/5m5x_3447_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A ARG 878": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 956": "NH1" <-> "NH2" Residue "A ARG 985": "NH1" <-> "NH2" Residue "A ARG 1003": "NH1" <-> "NH2" Residue "A ARG 1015": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1572": "NH1" <-> "NH2" Residue "A ARG 1580": "NH1" <-> "NH2" Residue "A ARG 1640": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B ARG 736": "NH1" <-> "NH2" Residue "B TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 908": "NH1" <-> "NH2" Residue "B ARG 909": "NH1" <-> "NH2" Residue "B ARG 920": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1065": "NH1" <-> "NH2" Residue "B ARG 1070": "NH1" <-> "NH2" Residue "B ARG 1130": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "G ARG 15": "NH1" <-> "NH2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "M ARG 31": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 16.28, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.88 Conformation dependent library (CDL) restraints added in 5.2 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: 10.27 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: 16.16 Time building geometry restraints manager: 13.07 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: 73.44 - 85.55: 2 85.55 - 97.66: 5 97.66 - 109.78: 4720 109.78 - 121.89: 35519 121.89 - 134.01: 7805 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 2.520 nonbonded pdb=" NH1 ARG A1105 " pdb=" OE2 GLU A1138 " model vdw 1.913 2.520 nonbonded pdb=" NZ LYS A1473 " pdb=" OE2 GLU A1475 " model vdw 1.931 2.520 nonbonded pdb=" O PHE A 248 " pdb=" OG1 THR A 249 " model vdw 1.946 2.440 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 ========== 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: 0.330 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: 3.570 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 95.870 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.120 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 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 35318 Z= 0.178 Angle : 0.641 39.242 48051 Z= 0.381 Chirality : 0.049 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 : 14.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.001 TRP B 836 HIS 0.003 0.001 HIS B 361 PHE 0.011 0.001 PHE E 72 TYR 0.012 0.001 TYR H 116 ARG 0.003 0.000 ARG B1063 *********************** 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 fitting. rotamer outliers: 52 poor density : 945 time to evaluate : 3.724 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: 0.5394 (pm20) REVERT: A 633 MET cc_start: 0.7111 (ptm) cc_final: 0.6486 (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: 0.7782 (tpt) cc_final: 0.7544 (tpt) REVERT: A 1613 MET cc_start: 0.5635 (mmt) cc_final: 0.5425 (mtp) REVERT: A 1646 LEU cc_start: 0.8224 (mt) cc_final: 0.7987 (mm) REVERT: B 45 HIS cc_start: 0.5594 (m90) cc_final: 0.5364 (m90) REVERT: B 541 LEU cc_start: 0.7067 (mt) cc_final: 0.6282 (pp) REVERT: B 690 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6277 (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: 0.6664 (tmt) REVERT: B 1074 MET cc_start: 0.7536 (mmt) cc_final: 0.7275 (mmm) REVERT: B 1133 MET cc_start: 0.5853 (tpp) cc_final: 0.5421 (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: 0.8307 (mmpt) cc_final: 0.7414 (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: 0.5067 time to fit residues: 781.7532 Evaluate side-chains 503 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 491 time to evaluate : 3.926 ------------------------------------------------------------------------------- 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 349 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 174 optimal weight: 0.4980 chunk 107 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 375 optimal weight: 0.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** 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 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN A 671 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1314 GLN A1443 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN B 770 ASN B 824 HIS B 896 GLN B 923 GLN B1034 GLN B1038 HIS C 53 ASN C 99 HIS C 130 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN E 99 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 35318 Z= 0.291 Angle : 0.710 9.527 48051 Z= 0.364 Chirality : 0.046 0.230 5380 Planarity : 0.005 0.064 5924 Dihedral : 14.281 171.612 5407 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.38 % Favored : 92.47 % Rotamer: Outliers : 4.06 % Allowed : 15.98 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.11), residues: 4063 helix: -1.86 (0.12), residues: 1264 sheet: -2.38 (0.19), residues: 561 loop : -2.66 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 79 HIS 0.010 0.002 HIS B 952 PHE 0.021 0.002 PHE B 440 TYR 0.050 0.003 TYR A1573 ARG 0.009 0.001 ARG C 100 *********************** 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 646 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 497 time to evaluate : 3.872 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 11 ILE cc_start: 0.7838 (mp) cc_final: 0.7563 (mt) REVERT: A 126 GLN cc_start: 0.7918 (mt0) cc_final: 0.7651 (tt0) REVERT: A 324 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5669 (mp) REVERT: A 458 GLN cc_start: 0.6241 (pm20) cc_final: 0.5851 (pm20) REVERT: A 618 TYR cc_start: 0.7573 (m-10) cc_final: 0.7097 (m-80) REVERT: A 633 MET cc_start: 0.7620 (ptm) cc_final: 0.7170 (mtm) REVERT: A 755 ILE cc_start: 0.4832 (OUTLIER) cc_final: 0.3966 (mt) REVERT: A 905 SER cc_start: 0.7448 (OUTLIER) cc_final: 0.7180 (t) REVERT: A 1132 TYR cc_start: 0.3339 (m-10) cc_final: 0.3109 (m-10) REVERT: A 1172 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7597 (tp) REVERT: A 1294 MET cc_start: 0.5303 (mmt) cc_final: 0.4063 (ptm) REVERT: A 1457 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.6151 (mt) REVERT: A 1519 LEU cc_start: 0.5176 (OUTLIER) cc_final: 0.4805 (tt) REVERT: A 1553 TYR cc_start: 0.8336 (m-80) cc_final: 0.8071 (m-80) REVERT: A 1588 MET cc_start: 0.7791 (tpt) cc_final: 0.7447 (tpt) REVERT: A 1613 MET cc_start: 0.6106 (mmt) cc_final: 0.5896 (mtp) REVERT: A 1617 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.7175 (p) REVERT: B 243 GLN cc_start: 0.4353 (pp30) cc_final: 0.4107 (pp30) REVERT: B 407 PHE cc_start: 0.6284 (OUTLIER) cc_final: 0.5684 (m-10) REVERT: B 690 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6659 (tt0) REVERT: B 858 ILE cc_start: 0.7053 (OUTLIER) cc_final: 0.6790 (tt) REVERT: B 1039 MET cc_start: 0.7804 (tmt) cc_final: 0.7003 (tmt) REVERT: B 1089 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8023 (tm-30) REVERT: B 1133 MET cc_start: 0.6337 (tpp) cc_final: 0.6127 (tpt) REVERT: C 101 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8378 (tp) REVERT: C 218 LYS cc_start: 0.7706 (pttt) cc_final: 0.7363 (pttp) REVERT: C 274 THR cc_start: 0.5520 (OUTLIER) cc_final: 0.4772 (t) REVERT: C 315 PHE cc_start: 0.6976 (m-80) cc_final: 0.6691 (m-80) REVERT: F 85 MET cc_start: 0.7756 (tpp) cc_final: 0.7032 (tpp) REVERT: F 122 MET cc_start: 0.6552 (mtp) cc_final: 0.6314 (mtm) REVERT: G 71 MET cc_start: 0.6050 (mpp) cc_final: 0.5582 (mmp) REVERT: G 126 GLN cc_start: 0.5016 (OUTLIER) cc_final: 0.3151 (mp10) REVERT: H 3 ASN cc_start: 0.7353 (t0) cc_final: 0.7024 (m-40) REVERT: H 128 ASN cc_start: 0.6927 (p0) cc_final: 0.6377 (p0) REVERT: J 52 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7716 (p) REVERT: K 110 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6008 (pt0) REVERT: K 125 MET cc_start: 0.7421 (ttp) cc_final: 0.7214 (mtp) REVERT: L 49 LYS cc_start: 0.8418 (mmpt) cc_final: 0.7631 (mttt) REVERT: N 57 LYS cc_start: 0.2053 (mmmt) cc_final: 0.1291 (ttpt) REVERT: N 90 MET cc_start: 0.3017 (mtm) cc_final: 0.2791 (mtm) outliers start: 149 outliers final: 72 residues processed: 616 average time/residue: 0.4641 time to fit residues: 468.2188 Evaluate side-chains 498 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 412 time to evaluate : 3.534 ------------------------------------------------------------------------------- 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 92 ASN 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 324 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 350 VAL 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 733 THR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1609 SER 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 249 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 330 LEU 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 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 512 LEU 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 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 1028 VAL Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 88 ASN 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 274 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain E residue 26 ARG 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 178 ILE Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 121 ASN 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 I residue 23 VAL Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 110 GLU 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 208 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 376 optimal weight: 0.0030 chunk 406 optimal weight: 0.0570 chunk 335 optimal weight: 7.9990 chunk 373 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 302 optimal weight: 9.9990 overall best weight: 1.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 332 GLN ** 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** A1191 GLN ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 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 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN G 10 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 ASN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN N 51 GLN ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35318 Z= 0.185 Angle : 0.630 10.899 48051 Z= 0.318 Chirality : 0.044 0.203 5380 Planarity : 0.005 0.061 5924 Dihedral : 14.337 172.631 5401 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.82 % Favored : 93.03 % Rotamer: Outliers : 4.47 % Allowed : 16.28 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.12), residues: 4063 helix: -1.20 (0.14), residues: 1272 sheet: -2.09 (0.19), residues: 589 loop : -2.42 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 143 HIS 0.010 0.001 HIS E 99 PHE 0.028 0.002 PHE A1297 TYR 0.022 0.002 TYR L 29 ARG 0.010 0.000 ARG E 17 *********************** 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 638 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 474 time to evaluate : 3.676 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: A 427 PHE cc_start: 0.6397 (m-80) cc_final: 0.5952 (m-80) REVERT: A 458 GLN cc_start: 0.6103 (pm20) cc_final: 0.5761 (pm20) REVERT: A 618 TYR cc_start: 0.7394 (m-10) cc_final: 0.7130 (m-80) REVERT: A 633 MET cc_start: 0.7639 (ptm) cc_final: 0.7152 (mtm) REVERT: A 635 MET cc_start: 0.8063 (tmm) cc_final: 0.7784 (tmm) REVERT: A 810 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7237 (mt) REVERT: A 1170 MET cc_start: 0.7099 (tpt) cc_final: 0.6746 (tpp) REVERT: A 1172 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7557 (tp) REVERT: A 1227 MET cc_start: 0.6958 (mmm) cc_final: 0.6754 (mmm) REVERT: A 1261 VAL cc_start: 0.6758 (t) cc_final: 0.6544 (t) REVERT: A 1262 LEU cc_start: 0.7605 (tp) cc_final: 0.6058 (mt) REVERT: A 1457 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.5881 (mt) REVERT: A 1493 CYS cc_start: 0.7226 (m) cc_final: 0.6886 (m) REVERT: A 1553 TYR cc_start: 0.8304 (m-80) cc_final: 0.8063 (m-80) REVERT: B 40 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6544 (mm-30) REVERT: B 45 HIS cc_start: 0.6181 (m90) cc_final: 0.5541 (m170) REVERT: B 270 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6798 (mp) REVERT: B 407 PHE cc_start: 0.6434 (OUTLIER) cc_final: 0.5869 (m-10) REVERT: B 690 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6653 (tt0) REVERT: B 1039 MET cc_start: 0.7835 (tmt) cc_final: 0.6876 (tmt) REVERT: B 1133 MET cc_start: 0.6155 (tpp) cc_final: 0.5855 (tpt) REVERT: B 1198 TYR cc_start: 0.6473 (m-80) cc_final: 0.6190 (m-80) REVERT: C 218 LYS cc_start: 0.7576 (pttt) cc_final: 0.7211 (pttp) REVERT: C 293 ARG cc_start: 0.7215 (mpt180) cc_final: 0.6987 (mpt180) REVERT: C 315 PHE cc_start: 0.6922 (m-80) cc_final: 0.6608 (m-80) REVERT: F 85 MET cc_start: 0.7835 (tpp) cc_final: 0.7071 (tpp) REVERT: G 71 MET cc_start: 0.6028 (mpp) cc_final: 0.5610 (mmp) REVERT: G 126 GLN cc_start: 0.5137 (OUTLIER) cc_final: 0.4082 (pp30) REVERT: H 3 ASN cc_start: 0.7313 (t0) cc_final: 0.6944 (m-40) REVERT: H 128 ASN cc_start: 0.6829 (p0) cc_final: 0.6384 (p0) REVERT: J 52 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7678 (p) REVERT: L 49 LYS cc_start: 0.8297 (mmpt) cc_final: 0.7626 (mtmt) REVERT: L 66 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8176 (tm-30) REVERT: N 57 LYS cc_start: 0.2076 (mmmt) cc_final: 0.1401 (ttpt) REVERT: N 107 MET cc_start: 0.5740 (mmm) cc_final: 0.4767 (pmm) outliers start: 164 outliers final: 90 residues processed: 602 average time/residue: 0.4369 time to fit residues: 436.5333 Evaluate side-chains 507 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 410 time to evaluate : 3.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL 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 350 VAL Chi-restraints excluded: chain A residue 402 ASP 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 674 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1016 SER 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 1198 THR Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1605 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 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 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 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 910 THR Chi-restraints excluded: chain B residue 915 ASP 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 1165 ASN Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 47 LEU 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 E residue 26 ARG 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 178 ILE 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 I residue 4 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 107 ASN 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 372 optimal weight: 0.6980 chunk 283 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 41 optimal weight: 0.0570 chunk 179 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 377 optimal weight: 6.9990 chunk 400 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 358 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS 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 718 GLN ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN E 99 HIS ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN N 51 GLN ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35318 Z= 0.212 Angle : 0.641 11.350 48051 Z= 0.324 Chirality : 0.044 0.216 5380 Planarity : 0.005 0.060 5924 Dihedral : 14.377 172.036 5398 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.63 % Favored : 92.22 % Rotamer: Outliers : 4.77 % Allowed : 17.26 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.12), residues: 4063 helix: -0.84 (0.14), residues: 1267 sheet: -1.90 (0.20), residues: 586 loop : -2.30 (0.12), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 143 HIS 0.009 0.001 HIS B 952 PHE 0.022 0.002 PHE A1068 TYR 0.023 0.002 TYR H 116 ARG 0.013 0.000 ARG A 422 *********************** 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 620 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 445 time to evaluate : 4.175 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: A 458 GLN cc_start: 0.6195 (pm20) cc_final: 0.5976 (pm20) REVERT: A 618 TYR cc_start: 0.7392 (m-10) cc_final: 0.7076 (m-80) REVERT: A 635 MET cc_start: 0.8094 (tmm) cc_final: 0.7869 (tmm) REVERT: A 830 MET cc_start: 0.8588 (tpt) cc_final: 0.8147 (tpt) REVERT: A 846 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7643 (mp) REVERT: A 1172 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7602 (tp) REVERT: A 1261 VAL cc_start: 0.6867 (t) cc_final: 0.6620 (t) REVERT: A 1457 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.5694 (mt) REVERT: A 1553 TYR cc_start: 0.8357 (m-80) cc_final: 0.8032 (m-80) REVERT: A 1611 MET cc_start: 0.8735 (tmm) cc_final: 0.8476 (tmm) REVERT: A 1613 MET cc_start: 0.6786 (mtp) cc_final: 0.6434 (mtt) REVERT: A 1617 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7070 (p) REVERT: B 270 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.6869 (mp) REVERT: B 407 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.5932 (m-10) REVERT: B 502 MET cc_start: 0.7742 (ttm) cc_final: 0.7269 (ttm) REVERT: B 690 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6355 (tt0) REVERT: B 721 MET cc_start: 0.6420 (mmp) cc_final: 0.5974 (mmp) REVERT: B 858 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6921 (mt) REVERT: B 1133 MET cc_start: 0.5844 (tpp) cc_final: 0.5484 (tpt) REVERT: C 47 LEU cc_start: 0.5384 (OUTLIER) cc_final: 0.4986 (tp) REVERT: C 218 LYS cc_start: 0.7871 (pttt) cc_final: 0.7433 (pttp) REVERT: C 293 ARG cc_start: 0.7347 (tpt170) cc_final: 0.6975 (mpt180) REVERT: C 315 PHE cc_start: 0.7044 (m-80) cc_final: 0.6742 (m-80) REVERT: D 44 ILE cc_start: 0.2336 (OUTLIER) cc_final: 0.2027 (mm) REVERT: E 215 MET cc_start: 0.4854 (mmt) cc_final: 0.4613 (mmm) REVERT: F 85 MET cc_start: 0.7879 (tpp) cc_final: 0.7058 (tpp) REVERT: F 100 GLN cc_start: 0.7612 (mt0) cc_final: 0.7384 (mt0) REVERT: G 126 GLN cc_start: 0.5248 (OUTLIER) cc_final: 0.4082 (pp30) REVERT: H 3 ASN cc_start: 0.7398 (t0) cc_final: 0.6918 (m-40) REVERT: H 11 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7657 (tm-30) REVERT: H 24 CYS cc_start: 0.7560 (m) cc_final: 0.7288 (p) REVERT: H 128 ASN cc_start: 0.6955 (p0) cc_final: 0.6586 (p0) REVERT: J 67 GLU cc_start: 0.6510 (mt-10) cc_final: 0.6296 (mt-10) REVERT: K 110 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5846 (pt0) REVERT: L 49 LYS cc_start: 0.8242 (mmpt) cc_final: 0.7634 (mtmt) REVERT: L 66 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8256 (tm-30) REVERT: M 31 ARG cc_start: 0.3420 (OUTLIER) cc_final: 0.2577 (ptp-170) outliers start: 175 outliers final: 108 residues processed: 578 average time/residue: 0.4421 time to fit residues: 427.1369 Evaluate side-chains 532 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 412 time to evaluate : 3.815 ------------------------------------------------------------------------------- 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 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 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 477 ASN Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 583 ASN 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 733 THR 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 1016 SER Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1070 LEU 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 1307 ASP Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1605 THR 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 31 ASP 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 259 THR 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 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 531 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 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 915 ASP 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 1109 SER Chi-restraints excluded: chain B residue 1165 ASN 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 97 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 90 VAL 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 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 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 J residue 13 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 333 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 297 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 341 optimal weight: 40.0000 chunk 276 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 359 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 671 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1567 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 231 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 684 ASN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** 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 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN K 106 GLN ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35318 Z= 0.242 Angle : 0.665 13.444 48051 Z= 0.337 Chirality : 0.045 0.226 5380 Planarity : 0.005 0.058 5924 Dihedral : 14.447 171.058 5397 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.27 % Favored : 91.58 % Rotamer: Outliers : 5.04 % Allowed : 18.11 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.12), residues: 4063 helix: -0.63 (0.14), residues: 1265 sheet: -1.82 (0.20), residues: 582 loop : -2.24 (0.12), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 530 HIS 0.008 0.001 HIS B 952 PHE 0.028 0.002 PHE J 8 TYR 0.022 0.002 TYR A1302 ARG 0.006 0.000 ARG H 19 *********************** 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 616 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 431 time to evaluate : 3.755 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 530 TRP cc_start: 0.6756 (t60) cc_final: 0.5952 (t60) REVERT: A 618 TYR cc_start: 0.7443 (m-10) cc_final: 0.7181 (m-80) REVERT: A 642 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7452 (t0) REVERT: A 830 MET cc_start: 0.8570 (tpt) cc_final: 0.8077 (tpp) REVERT: A 846 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7629 (mp) REVERT: A 905 SER cc_start: 0.7417 (OUTLIER) cc_final: 0.7161 (t) REVERT: A 1049 MET cc_start: 0.7866 (mtt) cc_final: 0.6974 (mmm) REVERT: A 1143 LYS cc_start: 0.8104 (ptpt) cc_final: 0.7855 (ptpt) REVERT: A 1172 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7769 (tp) REVERT: A 1178 LEU cc_start: 0.7949 (mm) cc_final: 0.7388 (mm) REVERT: A 1200 MET cc_start: 0.8285 (ttp) cc_final: 0.7888 (ttp) REVERT: A 1227 MET cc_start: 0.7201 (mmm) cc_final: 0.6926 (mmm) REVERT: A 1261 VAL cc_start: 0.7005 (t) cc_final: 0.6757 (t) REVERT: A 1262 LEU cc_start: 0.7030 (tp) cc_final: 0.5395 (mt) REVERT: A 1457 ILE cc_start: 0.6569 (OUTLIER) cc_final: 0.5725 (mt) REVERT: A 1553 TYR cc_start: 0.8335 (m-80) cc_final: 0.8070 (m-80) REVERT: A 1613 MET cc_start: 0.6373 (mtp) cc_final: 0.5977 (mtt) REVERT: A 1617 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7293 (p) REVERT: B 243 GLN cc_start: 0.4058 (pp30) cc_final: 0.3768 (pp30) REVERT: B 270 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7260 (mt) REVERT: B 407 PHE cc_start: 0.6452 (OUTLIER) cc_final: 0.5719 (m-10) REVERT: B 502 MET cc_start: 0.7829 (ttm) cc_final: 0.7333 (ttm) REVERT: B 608 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6261 (tt) REVERT: B 1111 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5162 (pp) REVERT: B 1133 MET cc_start: 0.6073 (tpp) cc_final: 0.5642 (tpt) REVERT: C 47 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.4333 (tp) REVERT: C 218 LYS cc_start: 0.7912 (pttt) cc_final: 0.7640 (pttp) REVERT: C 293 ARG cc_start: 0.7328 (mpt180) cc_final: 0.7097 (mpt180) REVERT: C 311 GLU cc_start: 0.6664 (mp0) cc_final: 0.6024 (mp0) REVERT: D 44 ILE cc_start: 0.2340 (OUTLIER) cc_final: 0.2031 (mm) REVERT: E 187 TYR cc_start: 0.8086 (t80) cc_final: 0.7854 (t80) REVERT: F 100 GLN cc_start: 0.7679 (mt0) cc_final: 0.7391 (mt0) REVERT: G 126 GLN cc_start: 0.5443 (OUTLIER) cc_final: 0.4272 (pp30) REVERT: H 3 ASN cc_start: 0.7448 (t0) cc_final: 0.6939 (m-40) REVERT: H 11 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7566 (tm-30) REVERT: H 128 ASN cc_start: 0.7026 (p0) cc_final: 0.6630 (p0) REVERT: I 17 LEU cc_start: 0.3294 (OUTLIER) cc_final: 0.2959 (mp) REVERT: K 110 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6173 (pt0) REVERT: K 125 MET cc_start: 0.7367 (tpp) cc_final: 0.7038 (tpp) REVERT: L 49 LYS cc_start: 0.8208 (mmpt) cc_final: 0.7686 (mtmt) REVERT: L 66 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8097 (tm-30) REVERT: M 31 ARG cc_start: 0.3518 (OUTLIER) cc_final: 0.2917 (ptp-170) REVERT: N 107 MET cc_start: 0.5220 (mmm) cc_final: 0.4928 (pmm) outliers start: 185 outliers final: 123 residues processed: 576 average time/residue: 0.4289 time to fit residues: 413.1277 Evaluate side-chains 535 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 396 time to evaluate : 3.790 ------------------------------------------------------------------------------- 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 251 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 346 SER 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 491 GLU 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 733 THR 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 905 SER Chi-restraints excluded: chain A residue 930 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 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 1198 THR Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 31 ASP 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 236 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 259 THR 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 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 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 626 ILE 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 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 1109 SER 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 1153 ILE Chi-restraints excluded: chain B residue 1165 ASN 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 97 LEU 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 D residue 44 ILE Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 90 VAL 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 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 116 THR Chi-restraints excluded: chain G residue 121 ASN 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 9 ILE 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 17 LEU 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 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 M residue 107 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 134 optimal weight: 1.9990 chunk 360 optimal weight: 3.9990 chunk 79 optimal weight: 0.2980 chunk 234 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 400 optimal weight: 10.0000 chunk 332 optimal weight: 0.0370 chunk 185 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 950 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 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN K 106 GLN N 41 ASN N 51 GLN ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35318 Z= 0.181 Angle : 0.637 11.852 48051 Z= 0.318 Chirality : 0.043 0.218 5380 Planarity : 0.004 0.056 5924 Dihedral : 14.400 172.384 5396 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.83 % Favored : 92.07 % Rotamer: Outliers : 4.61 % Allowed : 19.39 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.13), residues: 4063 helix: -0.42 (0.15), residues: 1261 sheet: -1.73 (0.20), residues: 576 loop : -2.11 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 143 HIS 0.027 0.001 HIS B 231 PHE 0.026 0.001 PHE A1297 TYR 0.022 0.002 TYR H 116 ARG 0.005 0.000 ARG H 19 *********************** 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 614 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 445 time to evaluate : 3.840 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 180 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7232 (mm-30) REVERT: A 683 LYS cc_start: 0.6355 (OUTLIER) cc_final: 0.5865 (ptmt) REVERT: A 692 TYR cc_start: 0.7367 (OUTLIER) cc_final: 0.5291 (t80) REVERT: A 1034 TYR cc_start: 0.6031 (m-80) cc_final: 0.5391 (m-80) REVERT: A 1049 MET cc_start: 0.7903 (mtt) cc_final: 0.7013 (mmm) REVERT: A 1053 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8125 (m-30) REVERT: A 1172 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7612 (tp) REVERT: A 1178 LEU cc_start: 0.7867 (mm) cc_final: 0.7295 (mm) REVERT: A 1227 MET cc_start: 0.7233 (mmm) cc_final: 0.6863 (mmm) REVERT: A 1261 VAL cc_start: 0.6984 (t) cc_final: 0.6762 (t) REVERT: A 1457 ILE cc_start: 0.6441 (OUTLIER) cc_final: 0.5636 (mt) REVERT: A 1553 TYR cc_start: 0.8269 (m-80) cc_final: 0.8033 (m-80) REVERT: A 1613 MET cc_start: 0.6614 (mtp) cc_final: 0.6292 (mtt) REVERT: A 1617 THR cc_start: 0.7392 (OUTLIER) cc_final: 0.6705 (p) REVERT: A 1659 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.6925 (tttm) REVERT: B 270 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7316 (mt) REVERT: B 407 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5994 (m-10) REVERT: B 502 MET cc_start: 0.7740 (ttm) cc_final: 0.7362 (ttm) REVERT: B 541 LEU cc_start: 0.7839 (mt) cc_final: 0.7475 (mp) REVERT: B 649 MET cc_start: 0.5042 (mmp) cc_final: 0.4811 (mmp) REVERT: B 920 ARG cc_start: 0.8460 (ttm170) cc_final: 0.8033 (ttp-110) REVERT: B 1111 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6059 (pp) REVERT: C 47 LEU cc_start: 0.4949 (OUTLIER) cc_final: 0.4369 (tp) REVERT: C 218 LYS cc_start: 0.7842 (pttt) cc_final: 0.7595 (pttp) REVERT: C 235 ILE cc_start: 0.7578 (mm) cc_final: 0.7058 (mm) REVERT: C 293 ARG cc_start: 0.7407 (tpt170) cc_final: 0.7124 (mpt180) REVERT: C 311 GLU cc_start: 0.6585 (mp0) cc_final: 0.5900 (mp0) REVERT: C 315 PHE cc_start: 0.7086 (m-80) cc_final: 0.6819 (m-80) REVERT: D 44 ILE cc_start: 0.2502 (OUTLIER) cc_final: 0.2228 (mm) REVERT: E 187 TYR cc_start: 0.8021 (t80) cc_final: 0.7817 (t80) REVERT: F 100 GLN cc_start: 0.7699 (mt0) cc_final: 0.7386 (mt0) REVERT: G 126 GLN cc_start: 0.5295 (OUTLIER) cc_final: 0.4087 (pp30) REVERT: H 3 ASN cc_start: 0.7367 (t0) cc_final: 0.6821 (m-40) REVERT: H 11 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7502 (tm-30) REVERT: H 128 ASN cc_start: 0.6637 (p0) cc_final: 0.6292 (p0) REVERT: K 110 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6159 (pt0) REVERT: L 49 LYS cc_start: 0.8347 (mmpt) cc_final: 0.7874 (mtmt) REVERT: L 66 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8061 (tm-30) REVERT: M 31 ARG cc_start: 0.3416 (OUTLIER) cc_final: 0.2820 (ptp-170) REVERT: N 107 MET cc_start: 0.5145 (mmm) cc_final: 0.4886 (pmm) outliers start: 169 outliers final: 116 residues processed: 582 average time/residue: 0.4707 time to fit residues: 460.3390 Evaluate side-chains 536 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 405 time to evaluate : 3.866 ------------------------------------------------------------------------------- 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 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 251 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 583 ASN 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 683 LYS Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 883 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 1044 THR Chi-restraints excluded: chain A residue 1053 ASP 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 1255 CYS Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1605 THR 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 A residue 1659 LYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 86 SER 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 236 ILE 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 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 446 MET Chi-restraints excluded: chain B residue 477 ASP 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 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 1010 ASN Chi-restraints excluded: chain B residue 1020 GLU Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1153 ILE Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 61 THR 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 204 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 69 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 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 116 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 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 13 VAL 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 26 PHE Chi-restraints excluded: chain M residue 31 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 386 optimal weight: 0.0470 chunk 45 optimal weight: 4.9990 chunk 228 optimal weight: 0.0000 chunk 292 optimal weight: 8.9990 chunk 226 optimal weight: 4.9990 chunk 337 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 399 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 overall best weight: 1.0088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS C 232 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN N 51 GLN ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35318 Z= 0.179 Angle : 0.643 11.441 48051 Z= 0.319 Chirality : 0.044 0.215 5380 Planarity : 0.004 0.056 5924 Dihedral : 14.401 172.639 5396 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.58 % Favored : 92.30 % Rotamer: Outliers : 4.55 % Allowed : 19.80 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.13), residues: 4063 helix: -0.28 (0.15), residues: 1266 sheet: -1.68 (0.20), residues: 579 loop : -2.03 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 530 HIS 0.029 0.001 HIS B 952 PHE 0.024 0.001 PHE A1297 TYR 0.020 0.002 TYR H 116 ARG 0.007 0.000 ARG B 210 *********************** 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 601 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 434 time to evaluate : 3.861 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 180 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7183 (mm-30) REVERT: A 211 THR cc_start: 0.5003 (OUTLIER) cc_final: 0.4756 (t) REVERT: A 618 TYR cc_start: 0.7199 (m-80) cc_final: 0.6999 (m-80) REVERT: A 683 LYS cc_start: 0.6373 (OUTLIER) cc_final: 0.5866 (ptmt) REVERT: A 692 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.5348 (t80) REVERT: A 868 THR cc_start: 0.7185 (p) cc_final: 0.6748 (t) REVERT: A 925 MET cc_start: 0.8475 (tpp) cc_final: 0.8208 (tpp) REVERT: A 1042 ASP cc_start: 0.5456 (OUTLIER) cc_final: 0.5245 (p0) REVERT: A 1049 MET cc_start: 0.7815 (mtt) cc_final: 0.6940 (mmm) REVERT: A 1053 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: A 1063 MET cc_start: 0.8409 (ttm) cc_final: 0.8189 (ttm) REVERT: A 1170 MET cc_start: 0.7249 (tpt) cc_final: 0.6889 (tpp) REVERT: A 1172 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7571 (tp) REVERT: A 1178 LEU cc_start: 0.7834 (mm) cc_final: 0.7242 (mm) REVERT: A 1261 VAL cc_start: 0.7071 (t) cc_final: 0.6835 (t) REVERT: A 1457 ILE cc_start: 0.6416 (OUTLIER) cc_final: 0.5628 (mt) REVERT: A 1553 TYR cc_start: 0.8255 (m-80) cc_final: 0.7973 (m-80) REVERT: A 1611 MET cc_start: 0.8824 (tmm) cc_final: 0.8585 (tmm) REVERT: A 1617 THR cc_start: 0.7317 (OUTLIER) cc_final: 0.6711 (p) REVERT: B 407 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.5932 (m-10) REVERT: B 502 MET cc_start: 0.7663 (ttm) cc_final: 0.7253 (ttm) REVERT: B 608 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6176 (tt) REVERT: B 649 MET cc_start: 0.5907 (mmp) cc_final: 0.5705 (mmp) REVERT: B 721 MET cc_start: 0.6280 (mmp) cc_final: 0.5939 (mmp) REVERT: B 920 ARG cc_start: 0.8465 (ttm170) cc_final: 0.8033 (ttp-110) REVERT: B 1111 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6013 (pp) REVERT: B 1133 MET cc_start: 0.5728 (tpt) cc_final: 0.5407 (tpt) REVERT: C 47 LEU cc_start: 0.5051 (OUTLIER) cc_final: 0.4445 (tp) REVERT: C 218 LYS cc_start: 0.7735 (pttt) cc_final: 0.7494 (pttp) REVERT: C 293 ARG cc_start: 0.7407 (tpt170) cc_final: 0.7141 (mpt180) REVERT: C 311 GLU cc_start: 0.6559 (mp0) cc_final: 0.5894 (mp0) REVERT: D 44 ILE cc_start: 0.2442 (OUTLIER) cc_final: 0.2198 (mm) REVERT: E 39 LEU cc_start: 0.8014 (mt) cc_final: 0.7688 (mt) REVERT: E 121 MET cc_start: 0.8113 (tpp) cc_final: 0.7854 (tpp) REVERT: F 100 GLN cc_start: 0.7844 (mt0) cc_final: 0.7536 (mt0) REVERT: G 126 GLN cc_start: 0.5297 (OUTLIER) cc_final: 0.4062 (pp30) REVERT: H 3 ASN cc_start: 0.7383 (t0) cc_final: 0.6831 (m-40) REVERT: H 11 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7796 (tm-30) REVERT: H 24 CYS cc_start: 0.7469 (m) cc_final: 0.7261 (p) REVERT: H 128 ASN cc_start: 0.6587 (p0) cc_final: 0.6241 (p0) REVERT: H 146 ARG cc_start: 0.5256 (OUTLIER) cc_final: 0.4656 (tmm160) REVERT: K 110 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.5861 (pt0) REVERT: L 49 LYS cc_start: 0.8345 (mmpt) cc_final: 0.7882 (mtmt) REVERT: L 66 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8063 (tm-30) REVERT: M 31 ARG cc_start: 0.3400 (OUTLIER) cc_final: 0.2800 (ptp-170) REVERT: N 107 MET cc_start: 0.5209 (mmm) cc_final: 0.4669 (pmm) outliers start: 167 outliers final: 118 residues processed: 564 average time/residue: 0.4436 time to fit residues: 416.8795 Evaluate side-chains 544 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 409 time to evaluate : 3.709 ------------------------------------------------------------------------------- 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 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 211 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 346 SER 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 477 ASN 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 583 ASN 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 683 LYS Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 972 TYR 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 1042 ASP Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1053 ASP 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 1255 CYS Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1605 THR 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 31 ASP Chi-restraints excluded: chain B residue 86 SER 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 236 ILE 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 446 MET 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 626 ILE 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 910 THR Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 990 ASP Chi-restraints excluded: chain B residue 1010 ASN Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 61 THR 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 204 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 69 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 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 169 VAL 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 23 VAL Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain K residue 65 ILE 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 26 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 107 ASN 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 246 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 77 optimal weight: 0.5980 chunk 253 optimal weight: 0.0000 chunk 271 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 37 optimal weight: 0.1980 chunk 313 optimal weight: 10.0000 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS ** 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** E 61 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN N 51 GLN ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35318 Z= 0.166 Angle : 0.643 11.938 48051 Z= 0.317 Chirality : 0.043 0.230 5380 Planarity : 0.004 0.054 5924 Dihedral : 14.369 173.345 5396 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.33 % Favored : 92.54 % Rotamer: Outliers : 3.68 % Allowed : 21.08 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.13), residues: 4063 helix: -0.22 (0.15), residues: 1269 sheet: -1.42 (0.21), residues: 591 loop : -1.92 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP E 13 HIS 0.027 0.001 HIS B 952 PHE 0.020 0.001 PHE C 36 TYR 0.035 0.001 TYR E 187 ARG 0.011 0.000 ARG B 261 *********************** 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 588 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 453 time to evaluate : 4.250 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: 0.7437 (mm-30) cc_final: 0.7147 (mm-30) REVERT: A 211 THR cc_start: 0.4838 (OUTLIER) cc_final: 0.4624 (t) REVERT: A 553 GLN cc_start: 0.6600 (OUTLIER) cc_final: 0.5603 (mm-40) REVERT: A 692 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.5247 (t80) REVERT: A 843 ARG cc_start: 0.7407 (ttm110) cc_final: 0.7067 (ttt90) REVERT: A 925 MET cc_start: 0.8288 (tpp) cc_final: 0.7718 (mmm) REVERT: A 1049 MET cc_start: 0.7743 (mtt) cc_final: 0.6925 (mmm) REVERT: A 1053 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7978 (m-30) REVERT: A 1170 MET cc_start: 0.7140 (tpt) cc_final: 0.6907 (tpp) REVERT: A 1172 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7513 (tp) REVERT: A 1178 LEU cc_start: 0.7758 (mm) cc_final: 0.7137 (mm) REVERT: A 1227 MET cc_start: 0.7121 (mmm) cc_final: 0.6785 (mmm) REVERT: A 1457 ILE cc_start: 0.6341 (OUTLIER) cc_final: 0.5576 (mt) REVERT: A 1553 TYR cc_start: 0.8156 (m-80) cc_final: 0.7879 (m-80) REVERT: A 1617 THR cc_start: 0.7202 (OUTLIER) cc_final: 0.6625 (p) REVERT: B 407 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.5836 (m-10) REVERT: B 502 MET cc_start: 0.7582 (ttm) cc_final: 0.7192 (ttm) REVERT: B 558 VAL cc_start: 0.4390 (OUTLIER) cc_final: 0.4178 (t) REVERT: B 690 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6093 (tt0) REVERT: B 1111 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6559 (mt) REVERT: B 1133 MET cc_start: 0.5484 (tpt) cc_final: 0.5116 (tpt) REVERT: C 47 LEU cc_start: 0.4943 (OUTLIER) cc_final: 0.4432 (tp) REVERT: C 218 LYS cc_start: 0.7667 (pttt) cc_final: 0.7424 (pttp) REVERT: C 293 ARG cc_start: 0.7425 (tpt170) cc_final: 0.7147 (mpt180) REVERT: C 311 GLU cc_start: 0.6649 (mp0) cc_final: 0.5895 (mp0) REVERT: C 315 PHE cc_start: 0.6675 (m-80) cc_final: 0.6423 (m-80) REVERT: E 58 MET cc_start: 0.5547 (tmm) cc_final: 0.4695 (ttp) REVERT: E 121 MET cc_start: 0.8071 (tpp) cc_final: 0.7847 (tpp) REVERT: F 100 GLN cc_start: 0.7713 (mt0) cc_final: 0.7447 (mt0) REVERT: G 118 CYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7178 (p) REVERT: G 126 GLN cc_start: 0.5272 (OUTLIER) cc_final: 0.4039 (pp30) REVERT: H 3 ASN cc_start: 0.7339 (t0) cc_final: 0.6772 (m-40) REVERT: H 11 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7753 (tm-30) REVERT: H 128 ASN cc_start: 0.6524 (p0) cc_final: 0.6087 (p0) REVERT: K 110 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.5702 (pt0) REVERT: L 49 LYS cc_start: 0.8326 (mmpt) cc_final: 0.7887 (mtmt) REVERT: L 66 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8153 (tm-30) REVERT: M 31 ARG cc_start: 0.3295 (OUTLIER) cc_final: 0.2711 (ptp-170) REVERT: N 107 MET cc_start: 0.4997 (mmm) cc_final: 0.4721 (pmm) outliers start: 135 outliers final: 103 residues processed: 554 average time/residue: 0.4535 time to fit residues: 414.8798 Evaluate side-chains 536 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 418 time to evaluate : 3.577 ------------------------------------------------------------------------------- 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 113 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 346 SER 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 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 561 LEU Chi-restraints excluded: chain A residue 583 ASN 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 692 TYR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 972 TYR 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 1044 THR Chi-restraints excluded: chain A residue 1053 ASP 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 1307 ASP Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1474 LEU 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 31 ASP Chi-restraints excluded: chain B residue 86 SER 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 236 ILE Chi-restraints excluded: chain B residue 274 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 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 673 ASN 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 990 ASP Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain E residue 69 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 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 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 3 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain K residue 65 ILE 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 M residue 60 LEU Chi-restraints excluded: chain M residue 67 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 362 optimal weight: 10.0000 chunk 382 optimal weight: 3.9990 chunk 348 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 336 optimal weight: 3.9990 chunk 351 optimal weight: 7.9990 chunk 370 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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** A 939 ASN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 ASN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN G 56 ASN G 59 GLN G 65 HIS H 21 ASN K 118 GLN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 35318 Z= 0.346 Angle : 0.767 12.220 48051 Z= 0.389 Chirality : 0.048 0.358 5380 Planarity : 0.005 0.066 5924 Dihedral : 14.614 168.622 5396 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.75 % Favored : 90.13 % Rotamer: Outliers : 4.53 % Allowed : 20.59 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.13), residues: 4063 helix: -0.49 (0.14), residues: 1276 sheet: -1.52 (0.21), residues: 559 loop : -2.11 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP E 13 HIS 0.033 0.002 HIS B 231 PHE 0.023 0.002 PHE J 8 TYR 0.032 0.003 TYR B1198 ARG 0.009 0.001 ARG B 134 *********************** 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 579 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 413 time to evaluate : 3.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7094 (mm-30) REVERT: A 470 HIS cc_start: 0.8144 (m-70) cc_final: 0.7642 (m170) REVERT: A 553 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.5762 (mm-40) REVERT: A 635 MET cc_start: 0.8166 (tmm) cc_final: 0.7832 (tmm) REVERT: A 683 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6438 (ptmt) REVERT: A 692 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.5791 (t80) REVERT: A 843 ARG cc_start: 0.7553 (ttm110) cc_final: 0.7017 (ttt-90) REVERT: A 905 SER cc_start: 0.7269 (OUTLIER) cc_final: 0.6976 (t) REVERT: A 1172 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7840 (tp) REVERT: A 1178 LEU cc_start: 0.8125 (mm) cc_final: 0.7526 (mm) REVERT: A 1457 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.5871 (mt) REVERT: A 1553 TYR cc_start: 0.8504 (m-80) cc_final: 0.8263 (m-80) REVERT: A 1611 MET cc_start: 0.8684 (tmm) cc_final: 0.8389 (tmm) REVERT: A 1617 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7600 (p) REVERT: B 407 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6077 (m-10) REVERT: B 436 MET cc_start: 0.4429 (ptp) cc_final: 0.4179 (ptp) REVERT: B 502 MET cc_start: 0.7979 (ttm) cc_final: 0.7636 (ttm) REVERT: B 541 LEU cc_start: 0.8091 (mt) cc_final: 0.7664 (mp) REVERT: B 591 LYS cc_start: 0.8027 (ptpt) cc_final: 0.7708 (ptpp) REVERT: B 721 MET cc_start: 0.6335 (mmp) cc_final: 0.6066 (mmp) REVERT: B 1111 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5102 (pp) REVERT: C 120 LEU cc_start: 0.6396 (mm) cc_final: 0.5944 (tp) REVERT: C 315 PHE cc_start: 0.7018 (m-80) cc_final: 0.6795 (m-80) REVERT: D 44 ILE cc_start: 0.2407 (OUTLIER) cc_final: 0.2193 (mm) REVERT: E 58 MET cc_start: 0.5910 (tmm) cc_final: 0.5326 (ttp) REVERT: E 121 MET cc_start: 0.8170 (tpp) cc_final: 0.7644 (tpp) REVERT: F 100 GLN cc_start: 0.7834 (mt0) cc_final: 0.7615 (mt0) REVERT: F 146 TRP cc_start: 0.6986 (m100) cc_final: 0.6760 (m100) REVERT: G 88 LYS cc_start: 0.7224 (tmtt) cc_final: 0.6990 (tttm) REVERT: G 118 CYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7009 (p) REVERT: G 126 GLN cc_start: 0.5130 (OUTLIER) cc_final: 0.3860 (pp30) REVERT: H 3 ASN cc_start: 0.7625 (t0) cc_final: 0.6980 (m-40) REVERT: H 11 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7568 (tm-30) REVERT: H 98 TYR cc_start: 0.8272 (t80) cc_final: 0.7718 (t80) REVERT: H 128 ASN cc_start: 0.6821 (p0) cc_final: 0.6450 (p0) REVERT: K 110 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6222 (pt0) REVERT: L 49 LYS cc_start: 0.8395 (mmpt) cc_final: 0.7968 (mtmt) REVERT: L 66 GLN cc_start: 0.8422 (tm-30) cc_final: 0.7883 (tm-30) REVERT: M 31 ARG cc_start: 0.3913 (OUTLIER) cc_final: 0.2899 (ptp-170) REVERT: N 107 MET cc_start: 0.5246 (mmm) cc_final: 0.4686 (pmm) outliers start: 166 outliers final: 124 residues processed: 547 average time/residue: 0.4683 time to fit residues: 432.8718 Evaluate side-chains 519 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 381 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 79 ILE 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 251 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 583 ASN 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 683 LYS Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 972 TYR 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 1198 THR Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1535 PHE Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 86 SER 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 236 ILE Chi-restraints excluded: chain B residue 275 MET 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 514 THR 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 673 ASN 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 990 ASP Chi-restraints excluded: chain B residue 1010 ASN Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1109 SER 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 1153 ILE Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 61 THR 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 44 ILE Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR 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 E residue 178 ILE Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 121 ASN 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 43 ASN Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 112 THR 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 M residue 60 LEU Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 107 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 5.9990 chunk 393 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 186 optimal weight: 0.0370 chunk 273 optimal weight: 0.0000 chunk 412 optimal weight: 5.9990 chunk 379 optimal weight: 5.9990 chunk 328 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 overall best weight: 2.0068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 ASN ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 35318 Z= 0.237 Angle : 0.714 16.110 48051 Z= 0.357 Chirality : 0.046 0.474 5380 Planarity : 0.005 0.068 5924 Dihedral : 14.574 170.923 5395 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.83 % Favored : 92.05 % Rotamer: Outliers : 3.82 % Allowed : 21.76 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.13), residues: 4063 helix: -0.38 (0.15), residues: 1267 sheet: -1.60 (0.21), residues: 580 loop : -2.02 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.003 TRP E 13 HIS 0.024 0.002 HIS B 231 PHE 0.020 0.002 PHE C 36 TYR 0.031 0.002 TYR E 187 ARG 0.009 0.001 ARG B 134 ********************** 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 561 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 421 time to evaluate : 4.152 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: 0.7392 (mm-30) cc_final: 0.7085 (mm-30) REVERT: A 530 TRP cc_start: 0.7088 (t60) cc_final: 0.6502 (t60) REVERT: A 553 GLN cc_start: 0.6505 (OUTLIER) cc_final: 0.5616 (mm-40) REVERT: A 683 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6088 (ptmt) REVERT: A 692 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.5458 (t80) REVERT: A 726 TRP cc_start: 0.7771 (m-90) cc_final: 0.7235 (m-90) REVERT: A 843 ARG cc_start: 0.7473 (ttm110) cc_final: 0.7057 (ttt90) REVERT: A 1170 MET cc_start: 0.7160 (tpt) cc_final: 0.6932 (tpp) REVERT: A 1172 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7666 (tp) REVERT: A 1178 LEU cc_start: 0.7808 (mm) cc_final: 0.7094 (mm) REVERT: A 1457 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.5806 (mt) REVERT: A 1553 TYR cc_start: 0.8382 (m-80) cc_final: 0.8125 (m-80) REVERT: A 1617 THR cc_start: 0.7546 (OUTLIER) cc_final: 0.6947 (p) REVERT: B 407 PHE cc_start: 0.6764 (OUTLIER) cc_final: 0.5955 (m-10) REVERT: B 436 MET cc_start: 0.4443 (ptp) cc_final: 0.4139 (ptp) REVERT: B 438 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7460 (pt) REVERT: B 502 MET cc_start: 0.7801 (ttm) cc_final: 0.7399 (ttm) REVERT: B 591 LYS cc_start: 0.7890 (ptpt) cc_final: 0.7571 (ptpp) REVERT: B 715 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8210 (m-40) REVERT: B 1111 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.5692 (pp) REVERT: C 293 ARG cc_start: 0.7628 (mmt180) cc_final: 0.7424 (mmt180) REVERT: C 315 PHE cc_start: 0.6859 (m-80) cc_final: 0.6629 (m-80) REVERT: D 44 ILE cc_start: 0.2315 (OUTLIER) cc_final: 0.2086 (mm) REVERT: E 121 MET cc_start: 0.8040 (tpp) cc_final: 0.7443 (tpp) REVERT: F 100 GLN cc_start: 0.7781 (mt0) cc_final: 0.7566 (mt0) REVERT: F 146 TRP cc_start: 0.6930 (m100) cc_final: 0.6727 (m100) REVERT: G 88 LYS cc_start: 0.7151 (tmtt) cc_final: 0.6896 (tttm) REVERT: G 118 CYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6977 (p) REVERT: G 126 GLN cc_start: 0.5360 (OUTLIER) cc_final: 0.3986 (pp30) REVERT: H 3 ASN cc_start: 0.7582 (t0) cc_final: 0.6895 (m-40) REVERT: H 11 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7612 (tm-30) REVERT: H 98 TYR cc_start: 0.8201 (t80) cc_final: 0.7649 (t80) REVERT: H 128 ASN cc_start: 0.6571 (p0) cc_final: 0.6210 (p0) REVERT: K 110 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6401 (pt0) REVERT: L 49 LYS cc_start: 0.8378 (mmpt) cc_final: 0.8021 (mtmt) REVERT: L 66 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8171 (tm-30) REVERT: M 31 ARG cc_start: 0.3826 (OUTLIER) cc_final: 0.2856 (ptp-170) REVERT: N 107 MET cc_start: 0.5578 (mmm) cc_final: 0.4937 (pmm) outliers start: 140 outliers final: 110 residues processed: 525 average time/residue: 0.4594 time to fit residues: 400.1736 Evaluate side-chains 513 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 388 time to evaluate : 3.672 ------------------------------------------------------------------------------- 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 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 346 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 583 ASN 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 683 LYS Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 972 TYR 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 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 1198 THR Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1535 PHE Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 86 SER 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 236 ILE 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 375 LEU 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 477 ASP 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 715 ASN 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 977 ILE Chi-restraints excluded: chain B residue 990 ASP Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1109 SER 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 1165 ASN 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 97 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 44 ILE 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 E residue 178 ILE Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 121 ASN 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 43 ASN Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 112 THR 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 M residue 60 LEU Chi-restraints excluded: chain M residue 67 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 260 optimal weight: 0.8980 chunk 349 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 302 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 328 optimal weight: 20.0000 chunk 137 optimal weight: 0.9980 chunk 337 optimal weight: 9.9990 chunk 41 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 344 GLN ** 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 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN N 41 ASN N 51 GLN ** N 85 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 = 0.4379 r_free = 0.4379 target = 0.181294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.162124 restraints weight = 62047.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.161254 restraints weight = 103541.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.162155 restraints weight = 83631.935| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35318 Z= 0.201 Angle : 0.694 16.094 48051 Z= 0.344 Chirality : 0.045 0.388 5380 Planarity : 0.005 0.102 5924 Dihedral : 14.529 172.060 5395 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.44 % Favored : 91.46 % Rotamer: Outliers : 3.41 % Allowed : 22.39 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.13), residues: 4063 helix: -0.32 (0.15), residues: 1273 sheet: -1.50 (0.21), residues: 578 loop : -1.97 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.003 TRP E 13 HIS 0.029 0.001 HIS B 231 PHE 0.026 0.002 PHE E 96 TYR 0.030 0.002 TYR E 187 ARG 0.009 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7890.84 seconds wall clock time: 144 minutes 27.59 seconds (8667.59 seconds total)