Starting phenix.real_space_refine (version: 1.21rc1) on Sun May 14 20:33:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5w_3446/05_2023/5m5w_3446_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5w_3446/05_2023/5m5w_3446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5w_3446/05_2023/5m5w_3446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5w_3446/05_2023/5m5w_3446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5w_3446/05_2023/5m5w_3446_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5w_3446/05_2023/5m5w_3446_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.013 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 7 6.06 5 P 43 5.49 5 S 172 5.16 5 C 21849 2.51 5 N 6036 2.21 5 O 6673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 422": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ARG 554": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 956": "NH1" <-> "NH2" Residue "A ARG 985": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1494": "NH1" <-> "NH2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1572": "NH1" <-> "NH2" Residue "A ARG 1580": "NH1" <-> "NH2" Residue "A ARG 1591": "NH1" <-> "NH2" Residue "A ARG 1631": "NH1" <-> "NH2" Residue "A ARG 1640": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ARG 550": "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 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 1070": "NH1" <-> "NH2" Residue "B ARG 1119": "NH1" <-> "NH2" Residue "B ARG 1130": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "N ARG 154": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 34780 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1493, 11760 Classifications: {'peptide': 1493} Link IDs: {'PCIS': 5, 'PTRANS': 56, 'TRANS': 1431} Chain breaks: 6 Chain: "B" Number of atoms: 9389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9389 Classifications: {'peptide': 1183} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1123} Chain breaks: 2 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: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1624 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain breaks: 1 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: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 869 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 109} Chain breaks: 1 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: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "N" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1164 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 136} Chain breaks: 3 Chain: "S" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 376 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "T" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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 75.111 102.030 28.646 1.00 88.95 S ATOM 806 SG CYS A 105 77.366 100.924 26.377 1.00 91.29 S ATOM 1624 SG CYS A 233 78.635 104.447 27.945 1.00 92.17 S ATOM 1646 SG CYS A 236 77.872 104.045 25.780 1.00104.79 S ATOM 461 SG CYS A 62 68.170 56.309 49.759 1.00 74.92 S ATOM 480 SG CYS A 65 71.296 54.770 50.767 1.00 72.34 S ATOM 535 SG CYS A 72 71.773 56.631 52.033 1.00 72.92 S ATOM 20429 SG CYS B1104 84.953 61.677 41.638 1.00 61.64 S ATOM 20455 SG CYS B1107 83.596 64.229 42.215 1.00 68.74 S ATOM 20602 SG CYS B1128 81.245 61.556 41.235 1.00 64.61 S ATOM 20630 SG CYS B1131 83.032 63.888 38.611 1.00 68.47 S ATOM 29392 SG CYS I 13 44.989 142.991 86.113 1.00141.37 S ATOM 29512 SG CYS I 30 45.554 143.205 82.082 1.00174.69 S ATOM 29962 SG CYS I 89 119.365 97.643 98.285 1.00169.58 S ATOM 30230 SG CYS J 7 82.009 62.074 122.929 1.00 81.98 S ATOM 30253 SG CYS J 10 83.987 59.970 124.958 1.00 77.69 S ATOM 30533 SG CYS J 45 85.747 62.694 125.416 1.00 81.16 S ATOM 30539 SG CYS J 46 83.207 60.579 126.183 1.00 81.59 S ATOM 31565 SG CYS L 31 41.240 60.992 106.439 1.00105.00 S ATOM 31585 SG CYS L 34 39.622 59.758 108.635 1.00107.07 S ATOM 31689 SG CYS L 48 38.029 60.686 104.447 1.00119.22 S ATOM 31712 SG CYS L 51 37.657 62.003 107.019 1.00115.61 S Time building chain proxies: 17.49, per 1000 atoms: 0.50 Number of scatterers: 34780 At special positions: 0 Unit cell: (162, 174.15, 166.05, 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 7 29.99 S 172 16.00 P 43 15.00 O 6673 8.00 N 6036 7.00 C 21849 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: 13.12 Conformation dependent library (CDL) restraints added in 4.8 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 233 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " 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 72 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " 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 I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" NE2 GLN I 88 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 27 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8026 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 49 sheets defined 33.4% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.843A pdb=" N ASN A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.531A pdb=" N LEU A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 removed outlier: 3.531A pdb=" N CYS A 120 " --> pdb=" O HIS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.850A pdb=" N LYS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 197 removed outlier: 3.581A pdb=" N LEU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 192 " --> pdb=" O TYR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'A' and resid 257 through 265 removed outlier: 3.876A pdb=" N ASN A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.917A pdb=" N PHE A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.420A 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 381 through 400 removed outlier: 4.006A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.549A pdb=" N LYS A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.738A pdb=" N GLN A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 500 through 505 removed outlier: 3.525A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.083A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 560 removed outlier: 3.756A pdb=" N ARG A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.702A pdb=" N MET A 600 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 removed outlier: 3.762A pdb=" N GLY A 622 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 671 through 681 removed outlier: 3.702A pdb=" N SER A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 removed outlier: 3.690A pdb=" N TYR A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 728 through 739 removed outlier: 3.707A pdb=" N VAL A 735 " --> pdb=" O ILE A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.758A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 824 Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 852 through 863 removed outlier: 3.676A pdb=" N ALA A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.784A pdb=" N GLU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 removed outlier: 3.538A pdb=" N LEU A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 930 Processing helix chain 'A' and resid 936 through 945 removed outlier: 4.011A pdb=" N GLN A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 943 " --> pdb=" O ASN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 980 removed outlier: 3.993A pdb=" N GLY A 980 " --> pdb=" O MET A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1008 removed outlier: 4.379A pdb=" N ASP A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1027 removed outlier: 3.913A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1065 through 1070 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 1108 removed outlier: 3.860A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A1096 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.730A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR A1127 " --> pdb=" O VAL A1123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1122 through 1127' Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.714A pdb=" N GLN A1141 " --> pdb=" O SER A1137 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A1150 " --> pdb=" O SER A1146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1177 removed outlier: 3.683A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1200 Proline residue: A1196 - end of helix Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1247 through 1254 removed outlier: 3.636A pdb=" N PHE A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1257 No H-bonds generated for 'chain 'A' and resid 1255 through 1257' Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 4.088A pdb=" N GLU A1305 " --> pdb=" O GLU A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.586A pdb=" N LEU A1313 " --> pdb=" O SER A1309 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A1318 " --> pdb=" O GLN A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1337 removed outlier: 3.746A pdb=" N ALA A1327 " --> pdb=" O HIS A1323 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS A1337 " --> pdb=" O ILE A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1452 Processing helix chain 'A' and resid 1485 through 1493 Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 3.586A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1554 Processing helix chain 'A' and resid 1554 through 1572 removed outlier: 3.874A pdb=" N ALA A1558 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A1564 " --> pdb=" O ASN A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 4.022A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP A1587 " --> pdb=" O ASP A1583 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A1590 " --> pdb=" O ALA A1586 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1605 removed outlier: 4.102A pdb=" N THR A1605 " --> pdb=" O GLY A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 3.617A pdb=" N TYR A1615 " --> pdb=" O MET A1611 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1627 removed outlier: 3.514A pdb=" N THR A1623 " --> pdb=" O CYS A1619 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A1625 " --> pdb=" O PHE A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1644 removed outlier: 4.456A pdb=" N VAL A1642 " --> pdb=" O SER A1638 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A1643 " --> pdb=" O ALA A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1653 Processing helix chain 'B' and resid 20 through 27 removed outlier: 3.529A pdb=" N ARG B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 42 through 54 removed outlier: 4.015A pdb=" N THR B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.591A pdb=" N GLY B 59 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 68 removed outlier: 3.540A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.546A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.956A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 284 through 290 removed outlier: 3.698A pdb=" N ILE B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.801A pdb=" N THR B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.715A pdb=" N LEU B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 3.603A pdb=" N LEU B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.795A pdb=" N LEU B 362 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 4.170A pdb=" N ARG B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR B 382 " --> pdb=" O ILE B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 406 through 435 removed outlier: 3.752A pdb=" N ASP B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 452 removed outlier: 3.540A pdb=" N ARG B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.684A pdb=" N PHE B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 579 through 583 removed outlier: 4.096A pdb=" N SER B 582 " --> pdb=" O ALA B 579 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 583 " --> pdb=" O GLY B 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 579 through 583' Processing helix chain 'B' and resid 597 through 612 Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.564A pdb=" N ASN B 695 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 697 " --> pdb=" O THR B 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 697' Processing helix chain 'B' and resid 711 through 724 removed outlier: 3.745A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 960 through 976 removed outlier: 3.618A pdb=" N LYS B 970 " --> pdb=" O SER B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1002 removed outlier: 3.932A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1080 removed outlier: 3.868A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1083 No H-bonds generated for 'chain 'B' and resid 1081 through 1083' Processing helix chain 'B' and resid 1084 through 1093 removed outlier: 3.953A pdb=" N LEU B1088 " --> pdb=" O THR B1084 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP B1090 " --> pdb=" O PHE B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1193 removed outlier: 3.866A pdb=" N LYS B1183 " --> pdb=" O PRO B1179 " (cutoff:3.500A) removed outlier: 3.694A 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: 3.598A pdb=" N SER C 73 " --> pdb=" O ARG C 69 " (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 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 251 removed outlier: 4.026A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 311 through 330 removed outlier: 3.927A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 44 removed outlier: 3.872A pdb=" N VAL D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.695A pdb=" N ILE D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 26 removed outlier: 3.538A pdb=" N ARG E 17 " --> pdb=" O TRP E 13 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.715A pdb=" N GLU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.846A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.571A pdb=" N LYS E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.519A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.684A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 4.048A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 56 through 73 removed outlier: 3.556A pdb=" N ILE F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG F 65 " --> pdb=" O HIS F 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA F 73 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'G' and resid 13 through 21 removed outlier: 3.570A pdb=" N LYS G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.524A pdb=" N LEU G 54 " --> pdb=" O PRO G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 63 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.518A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 removed outlier: 3.599A pdb=" N LYS I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 60 through 65' Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.796A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.540A pdb=" N ARG J 48 " --> pdb=" O TYR J 44 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.460A 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 82 removed outlier: 3.694A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE K 80 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET K 81 " --> pdb=" O ARG K 77 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 141 removed outlier: 3.989A pdb=" N ALA K 116 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL K 130 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE K 135 " --> pdb=" O VAL K 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 removed outlier: 3.664A pdb=" N ARG N 154 " --> pdb=" O TYR N 150 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 5.225A pdb=" N ILE A 11 " --> pdb=" O GLU B1201 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU B1201 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER A 13 " --> pdb=" O ASN B1199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.646A pdb=" N GLY A 77 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 476 Processing sheet with id=AA5, first strand: chain 'A' and resid 480 through 486 removed outlier: 7.823A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN A 590 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 634 " --> pdb=" O ASN A 590 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 633 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.363A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA8, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.729A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1031 through 1032 Processing sheet with id=AB1, first strand: chain 'A' and resid 1237 through 1238 Processing sheet with id=AB2, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 7.089A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1457 through 1462 removed outlier: 7.019A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A1461 " --> pdb=" O GLU A1471 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AB5, first strand: chain 'B' and resid 97 through 106 removed outlier: 4.224A pdb=" N GLU B 100 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LYS B 106 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ARG B 134 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TRP B 143 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE B 153 " --> pdb=" O TRP B 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 194 through 195 removed outlier: 3.633A pdb=" N LYS B 201 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 206 through 209 removed outlier: 3.601A pdb=" N LEU B 206 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 234 through 239 removed outlier: 5.893A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 502 through 503 Processing sheet with id=AC1, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC2, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC3, first strand: chain 'B' and resid 571 through 572 removed outlier: 4.096A pdb=" N ALA B 571 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TRP B 595 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 596 " --> pdb=" O CYS B 584 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 740 through 744 removed outlier: 4.158A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 740 through 744 removed outlier: 4.158A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS L 58 " --> pdb=" O VAL B 885 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 787 through 789 removed outlier: 3.778A pdb=" N ILE B 947 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B 771 " --> pdb=" O VAL B1031 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 918 " --> pdb=" O GLN B1034 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 787 through 789 removed outlier: 3.778A pdb=" N ILE B 947 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B 771 " --> pdb=" O VAL B1031 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 823 through 825 removed outlier: 4.125A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 872 " --> pdb=" O CYS B 859 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 861 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 870 " --> pdb=" O TYR B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD1, first strand: chain 'B' and resid 1099 through 1104 removed outlier: 3.553A pdb=" N THR B1174 " --> pdb=" O VAL B1103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD3, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AD4, first strand: chain 'C' and resid 42 through 46 removed outlier: 5.094A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 290 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.982A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 11.321A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.807A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU C 201 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASN C 87 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.602A pdb=" N THR C 141 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.622A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AD9, first strand: chain 'D' and resid 22 through 24 Processing sheet with id=AE1, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.923A pdb=" N ASN G 121 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLY G 86 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N TYR G 123 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR G 84 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N TRP G 125 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU G 82 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY G 79 " --> pdb=" O ASN G 74 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.229A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE4, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'G' and resid 131 through 140 removed outlier: 6.331A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE G 145 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE G 157 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU G 147 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE G 149 " --> pdb=" O PHE G 153 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP G 131 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.949A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP H 41 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU H 125 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR H 102 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR H 95 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA H 60 " --> pdb=" O TYR H 141 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AE8, first strand: chain 'I' and resid 110 through 113 removed outlier: 3.642A pdb=" N VAL I 110 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF1, first strand: chain 'M' and resid 87 through 88 removed outlier: 8.634A pdb=" N ILE M 88 " --> pdb=" O GLU M 9 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU M 11 " --> pdb=" O ILE M 88 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 54 through 56 removed outlier: 6.931A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA M 22 " --> pdb=" O LEU N 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 80 through 81 removed outlier: 4.173A pdb=" N ILE N 56 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL M 77 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE N 58 " --> pdb=" O GLN M 75 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 80 through 81 removed outlier: 6.299A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET N 80 " --> pdb=" O TYR N 87 " (cutoff:3.500A) 1115 hydrogen bonds defined for protein. 3078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.63 Time building geometry restraints manager: 14.35 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: 10661 1.34 - 1.45: 4977 1.45 - 1.57: 19541 1.57 - 1.69: 88 1.69 - 1.81: 271 Bond restraints: 35538 Sorted by residual: bond pdb=" N ASP K 57 " pdb=" CA ASP K 57 " ideal model delta sigma weight residual 1.458 1.663 -0.205 1.27e-02 6.20e+03 2.61e+02 bond pdb=" CA LYS A 250 " pdb=" C LYS A 250 " ideal model delta sigma weight residual 1.523 1.370 0.153 1.34e-02 5.57e+03 1.31e+02 bond pdb=" N LYS B1064 " pdb=" CA LYS B1064 " ideal model delta sigma weight residual 1.458 1.556 -0.098 1.30e-02 5.92e+03 5.71e+01 bond pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 1.532 1.650 -0.119 1.62e-02 3.81e+03 5.36e+01 bond pdb=" CA GLY K 58 " pdb=" C GLY K 58 " ideal model delta sigma weight residual 1.514 1.430 0.084 1.41e-02 5.03e+03 3.55e+01 ... (remaining 35533 not shown) Histogram of bond angle deviations from ideal: 73.12 - 85.34: 2 85.34 - 97.57: 3 97.57 - 109.79: 4408 109.79 - 122.02: 36333 122.02 - 134.25: 7448 Bond angle restraints: 48194 Sorted by residual: angle pdb=" N LYS B1064 " pdb=" CA LYS B1064 " pdb=" C LYS B1064 " ideal model delta sigma weight residual 113.55 79.37 34.18 1.26e+00 6.30e-01 7.36e+02 angle pdb=" N ASP K 57 " pdb=" CA ASP K 57 " pdb=" C ASP K 57 " ideal model delta sigma weight residual 112.04 73.12 38.92 1.44e+00 4.82e-01 7.31e+02 angle pdb=" C ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 110.56 86.70 23.86 1.83e+00 2.99e-01 1.70e+02 angle pdb=" N ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 110.19 95.87 14.32 1.55e+00 4.16e-01 8.53e+01 angle pdb=" C LYS B1064 " pdb=" CA LYS B1064 " pdb=" CB LYS B1064 " ideal model delta sigma weight residual 109.34 95.81 13.53 1.55e+00 4.16e-01 7.62e+01 ... (remaining 48189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 19941 17.17 - 34.35: 1162 34.35 - 51.52: 317 51.52 - 68.70: 79 68.70 - 85.87: 12 Dihedral angle restraints: 21511 sinusoidal: 9091 harmonic: 12420 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 -84.74 -37.86 0 2.50e+00 1.60e-01 2.29e+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 -93.68 -28.92 0 2.50e+00 1.60e-01 1.34e+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 97.16 25.64 0 2.50e+00 1.60e-01 1.05e+02 ... (remaining 21508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.291: 5374 0.291 - 0.582: 4 0.582 - 0.873: 0 0.873 - 1.164: 1 1.164 - 1.455: 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 3.97 -1.46 2.00e-01 2.50e+01 5.29e+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 3.63 -1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA LYS A 250 " pdb=" N LYS A 250 " pdb=" C LYS A 250 " pdb=" CB LYS A 250 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.54e+00 ... (remaining 5377 not shown) Planarity restraints: 6085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY K 58 " 0.028 2.00e-02 2.50e+03 5.42e-02 2.94e+01 pdb=" C GLY K 58 " -0.094 2.00e-02 2.50e+03 pdb=" O GLY K 58 " 0.032 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=" CA ASP A 246 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.96e+00 pdb=" C ASP A 246 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP A 246 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY A 247 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 341 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO B 342 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 342 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 342 " -0.029 5.00e-02 4.00e+02 ... (remaining 6082 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.10: 6 2.10 - 2.80: 9457 2.80 - 3.50: 46755 3.50 - 4.20: 81841 4.20 - 4.90: 137250 Nonbonded interactions: 275309 Sorted by model distance: nonbonded pdb=" O LYS B1061 " pdb=" NH2 ARG B1065 " model vdw 1.405 2.520 nonbonded pdb=" OH TYR H 98 " pdb=" OD1 ASN H 139 " model vdw 1.424 2.440 nonbonded pdb=" O SER A 764 " pdb=" N GLU A 766 " model vdw 1.934 2.520 nonbonded pdb=" N ASP K 57 " pdb=" N GLY K 58 " model vdw 1.984 2.560 nonbonded pdb=" CE1 PHE A 248 " pdb=" NZ LYS A 442 " model vdw 2.035 3.420 ... (remaining 275304 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: 0.280 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: 4.380 Check model and map are aligned: 0.520 Set scattering table: 0.290 Process input model: 93.470 Find NCS groups from input model: 0.910 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 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 0.205 35538 Z= 0.177 Angle : 0.615 38.922 48194 Z= 0.358 Chirality : 0.049 1.455 5380 Planarity : 0.004 0.057 6085 Dihedral : 12.179 85.873 13485 Min Nonbonded Distance : 1.405 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.27 % Favored : 95.61 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.08 % 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: -4.15 (0.11), residues: 4211 helix: -3.31 (0.10), residues: 1186 sheet: -2.26 (0.20), residues: 545 loop : -2.66 (0.11), residues: 2480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1084 time to evaluate : 4.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 4 residues processed: 1116 average time/residue: 0.5185 time to fit residues: 908.3223 Evaluate side-chains 616 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 612 time to evaluate : 4.044 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4813 time to fit residues: 9.1691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 358 optimal weight: 10.0000 chunk 321 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 332 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 202 optimal weight: 10.0000 chunk 247 optimal weight: 0.5980 chunk 385 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 425 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 571 HIS ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS A 673 HIS ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1141 GLN A1250 GLN ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 248 ASN B 282 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 683 ASN B 688 HIS B 702 ASN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN B 764 ASN B 767 ASN B 867 ASN B 886 ASN B 923 GLN B 944 GLN ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 207 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 49 ASN D 88 GLN E 54 GLN E 143 ASN E 146 HIS F 59 GLN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS H 33 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 ASN J 53 HIS ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 35538 Z= 0.281 Angle : 0.678 13.499 48194 Z= 0.346 Chirality : 0.045 0.213 5380 Planarity : 0.005 0.065 6085 Dihedral : 10.331 82.574 5046 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.89 % Favored : 94.09 % Rotamer Outliers : 4.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -3.00 (0.12), residues: 4211 helix: -1.74 (0.13), residues: 1195 sheet: -1.90 (0.19), residues: 585 loop : -2.19 (0.12), residues: 2431 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 653 time to evaluate : 4.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 181 outliers final: 85 residues processed: 795 average time/residue: 0.4836 time to fit residues: 624.7712 Evaluate side-chains 635 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 550 time to evaluate : 4.089 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 0 residues processed: 85 average time/residue: 0.3233 time to fit residues: 57.2151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 213 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 chunk 320 optimal weight: 0.2980 chunk 262 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 385 optimal weight: 6.9990 chunk 416 optimal weight: 0.3980 chunk 343 optimal weight: 0.8980 chunk 382 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 515 ASN ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1250 GLN A1453 HIS B 209 GLN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 GLN C 88 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN I 32 GLN I 95 ASN J 23 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 HIS ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 35538 Z= 0.205 Angle : 0.631 12.804 48194 Z= 0.317 Chirality : 0.044 0.246 5380 Planarity : 0.005 0.077 6085 Dihedral : 10.312 82.625 5046 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.22 % Favored : 94.75 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -2.51 (0.12), residues: 4211 helix: -1.05 (0.14), residues: 1205 sheet: -1.75 (0.19), residues: 601 loop : -2.00 (0.12), residues: 2405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 618 time to evaluate : 3.923 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 outliers start: 98 outliers final: 31 residues processed: 698 average time/residue: 0.4830 time to fit residues: 549.1367 Evaluate side-chains 580 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 549 time to evaluate : 4.037 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3410 time to fit residues: 25.2657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 381 optimal weight: 0.5980 chunk 290 optimal weight: 0.4980 chunk 200 optimal weight: 5.9990 chunk 42 optimal weight: 0.0670 chunk 184 optimal weight: 6.9990 chunk 259 optimal weight: 0.9990 chunk 387 optimal weight: 1.9990 chunk 409 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 366 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B 952 HIS B 975 HIS C 99 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 HIS ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 35538 Z= 0.168 Angle : 0.613 12.011 48194 Z= 0.304 Chirality : 0.043 0.227 5380 Planarity : 0.004 0.054 6085 Dihedral : 10.265 82.232 5046 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.37 % Favored : 94.61 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -2.18 (0.12), residues: 4211 helix: -0.63 (0.14), residues: 1209 sheet: -1.54 (0.19), residues: 606 loop : -1.89 (0.12), residues: 2396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 594 time to evaluate : 4.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 33 residues processed: 650 average time/residue: 0.5082 time to fit residues: 543.5554 Evaluate side-chains 576 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 543 time to evaluate : 4.298 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3445 time to fit residues: 26.9930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 341 optimal weight: 0.2980 chunk 232 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 305 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 349 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 367 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 HIS ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 HIS N 106 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.087 35538 Z= 0.454 Angle : 0.791 14.431 48194 Z= 0.403 Chirality : 0.050 0.287 5380 Planarity : 0.006 0.078 6085 Dihedral : 10.647 81.197 5046 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.93 % Favored : 92.00 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -2.44 (0.12), residues: 4211 helix: -0.93 (0.14), residues: 1222 sheet: -1.66 (0.20), residues: 589 loop : -2.03 (0.12), residues: 2400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 555 time to evaluate : 3.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 66 residues processed: 637 average time/residue: 0.4692 time to fit residues: 489.8392 Evaluate side-chains 565 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 499 time to evaluate : 4.090 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.3445 time to fit residues: 47.3887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 137 optimal weight: 0.9980 chunk 369 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 240 optimal weight: 0.0570 chunk 101 optimal weight: 9.9990 chunk 410 optimal weight: 20.0000 chunk 340 optimal weight: 20.0000 chunk 189 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 135 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 378 HIS ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 35538 Z= 0.182 Angle : 0.648 12.147 48194 Z= 0.322 Chirality : 0.044 0.195 5380 Planarity : 0.004 0.055 6085 Dihedral : 10.385 81.810 5046 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.30 % Favored : 94.68 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -2.01 (0.12), residues: 4211 helix: -0.48 (0.15), residues: 1220 sheet: -1.38 (0.20), residues: 580 loop : -1.81 (0.12), residues: 2411 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 582 time to evaluate : 4.502 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 17 residues processed: 622 average time/residue: 0.5080 time to fit residues: 522.8891 Evaluate side-chains 538 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 521 time to evaluate : 3.871 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3144 time to fit residues: 15.6602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 395 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 233 optimal weight: 0.1980 chunk 299 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 345 optimal weight: 30.0000 chunk 229 optimal weight: 9.9990 chunk 408 optimal weight: 6.9990 chunk 255 optimal weight: 2.9990 chunk 249 optimal weight: 0.6980 chunk 188 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 ASN ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 35538 Z= 0.234 Angle : 0.661 10.997 48194 Z= 0.329 Chirality : 0.045 0.220 5380 Planarity : 0.004 0.057 6085 Dihedral : 10.361 80.802 5046 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.46 % Favored : 93.52 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -1.91 (0.12), residues: 4211 helix: -0.37 (0.15), residues: 1223 sheet: -1.29 (0.21), residues: 580 loop : -1.78 (0.12), residues: 2408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 552 time to evaluate : 3.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 28 residues processed: 584 average time/residue: 0.4799 time to fit residues: 461.5634 Evaluate side-chains 545 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 517 time to evaluate : 4.312 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3750 time to fit residues: 24.7461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 252 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 278 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 321 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS G 56 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 35538 Z= 0.263 Angle : 0.679 12.617 48194 Z= 0.339 Chirality : 0.045 0.201 5380 Planarity : 0.004 0.058 6085 Dihedral : 10.385 80.930 5046 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.53 % Favored : 93.45 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -1.86 (0.12), residues: 4211 helix: -0.35 (0.15), residues: 1210 sheet: -1.20 (0.21), residues: 569 loop : -1.75 (0.12), residues: 2432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 538 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 23 residues processed: 565 average time/residue: 0.4717 time to fit residues: 441.2177 Evaluate side-chains 537 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 514 time to evaluate : 4.241 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3648 time to fit residues: 21.1540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 371 optimal weight: 9.9990 chunk 391 optimal weight: 7.9990 chunk 357 optimal weight: 9.9990 chunk 380 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 165 optimal weight: 0.0970 chunk 299 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 344 optimal weight: 3.9990 chunk 360 optimal weight: 8.9990 chunk 379 optimal weight: 0.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 35538 Z= 0.268 Angle : 0.686 12.476 48194 Z= 0.344 Chirality : 0.045 0.244 5380 Planarity : 0.005 0.083 6085 Dihedral : 10.410 81.713 5046 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.60 % Favored : 93.37 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -1.83 (0.12), residues: 4211 helix: -0.34 (0.15), residues: 1216 sheet: -1.28 (0.21), residues: 587 loop : -1.69 (0.12), residues: 2408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 530 time to evaluate : 3.930 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 17 residues processed: 551 average time/residue: 0.4908 time to fit residues: 446.0868 Evaluate side-chains 525 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 508 time to evaluate : 3.882 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3346 time to fit residues: 16.5884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 250 optimal weight: 0.7980 chunk 402 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 chunk 422 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 336 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 35538 Z= 0.230 Angle : 0.679 11.899 48194 Z= 0.339 Chirality : 0.045 0.232 5380 Planarity : 0.004 0.078 6085 Dihedral : 10.378 81.580 5046 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.13 % Favored : 93.85 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -1.78 (0.12), residues: 4211 helix: -0.32 (0.15), residues: 1225 sheet: -1.18 (0.21), residues: 572 loop : -1.66 (0.12), residues: 2414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 538 time to evaluate : 4.033 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 544 average time/residue: 0.4887 time to fit residues: 437.0707 Evaluate side-chains 528 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 512 time to evaluate : 4.064 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4086 time to fit residues: 17.3069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.7283 > 50: distance: 45 - 68: 7.643 distance: 50 - 79: 31.689 distance: 58 - 85: 25.978 distance: 63 - 68: 6.254 distance: 68 - 69: 7.055 distance: 69 - 70: 20.937 distance: 69 - 72: 9.596 distance: 70 - 71: 3.998 distance: 70 - 79: 5.457 distance: 72 - 73: 9.453 distance: 73 - 74: 6.397 distance: 73 - 75: 6.065 distance: 74 - 76: 6.871 distance: 75 - 77: 4.854 distance: 76 - 78: 6.397 distance: 79 - 80: 19.160 distance: 80 - 81: 26.404 distance: 80 - 83: 46.412 distance: 81 - 82: 12.407 distance: 81 - 85: 37.909 distance: 85 - 86: 7.319 distance: 86 - 87: 25.273 distance: 86 - 89: 17.108 distance: 87 - 88: 9.292 distance: 87 - 96: 27.159 distance: 89 - 90: 11.829 distance: 90 - 91: 25.917 distance: 91 - 92: 4.103 distance: 92 - 93: 25.631 distance: 93 - 95: 7.875 distance: 97 - 98: 30.600 distance: 97 - 100: 4.586 distance: 98 - 99: 14.185 distance: 98 - 108: 20.581 distance: 100 - 101: 12.540 distance: 101 - 102: 9.360 distance: 101 - 103: 30.241 distance: 102 - 104: 24.614 distance: 103 - 105: 7.113 distance: 104 - 106: 36.893 distance: 105 - 106: 32.252 distance: 106 - 107: 19.012 distance: 108 - 109: 8.695 distance: 109 - 110: 11.240 distance: 109 - 112: 42.998 distance: 110 - 111: 42.762 distance: 110 - 113: 26.338 distance: 113 - 114: 7.310 distance: 114 - 115: 12.410 distance: 114 - 117: 31.039 distance: 115 - 116: 3.899 distance: 115 - 121: 7.789 distance: 117 - 118: 19.102 distance: 117 - 119: 43.390 distance: 118 - 120: 5.969 distance: 121 - 122: 30.914 distance: 122 - 123: 21.355 distance: 122 - 125: 27.810 distance: 123 - 124: 16.356 distance: 123 - 127: 29.092 distance: 125 - 126: 16.128 distance: 127 - 128: 13.840 distance: 128 - 129: 18.467 distance: 128 - 131: 27.030 distance: 129 - 130: 21.843 distance: 129 - 134: 24.486 distance: 134 - 135: 29.446 distance: 135 - 136: 35.199 distance: 135 - 138: 31.891 distance: 136 - 137: 5.813 distance: 136 - 140: 32.188 distance: 138 - 139: 7.357 distance: 140 - 141: 16.503 distance: 141 - 142: 4.838 distance: 141 - 144: 24.396 distance: 142 - 143: 3.738 distance: 142 - 151: 30.108 distance: 143 - 174: 25.093 distance: 144 - 145: 16.214 distance: 145 - 147: 9.242 distance: 146 - 148: 12.897 distance: 147 - 149: 5.059 distance: 148 - 150: 17.010