Starting phenix.real_space_refine on Thu Feb 22 16:38:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5w_3446/02_2024/5m5w_3446_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5w_3446/02_2024/5m5w_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_3446/02_2024/5m5w_3446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5w_3446/02_2024/5m5w_3446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5w_3446/02_2024/5m5w_3446_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5w_3446/02_2024/5m5w_3446_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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-dev-5238/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: 17.84, per 1000 atoms: 0.51 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: 12.87 Conformation dependent library (CDL) restraints added in 5.9 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: 4.57 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: 15.07 Time building geometry restraints manager: 13.97 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: 19961 17.17 - 34.35: 1182 34.35 - 51.52: 327 51.52 - 68.70: 81 68.70 - 85.87: 12 Dihedral angle restraints: 21563 sinusoidal: 9143 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 21560 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 3.100 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 95.130 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.570 ------------------------------------------------------------------------------- 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 : 12.280 85.873 13537 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 % Allowed : 11.39 % Favored : 87.27 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 264 HIS 0.004 0.000 HIS A 116 PHE 0.009 0.001 PHE M 81 TYR 0.010 0.001 TYR B 655 ARG 0.004 0.000 ARG H 130 *********************** 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 : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7952 (pttt) cc_final: 0.7257 (pttm) REVERT: A 182 LYS cc_start: 0.6842 (tppt) cc_final: 0.6569 (ttpt) REVERT: A 191 MET cc_start: 0.7450 (ppp) cc_final: 0.7172 (ppp) REVERT: A 199 ASP cc_start: 0.6566 (p0) cc_final: 0.6248 (p0) REVERT: A 446 ARG cc_start: 0.4931 (OUTLIER) cc_final: 0.3899 (mmp-170) REVERT: A 540 ASP cc_start: 0.8410 (t70) cc_final: 0.8146 (t0) REVERT: A 914 ASP cc_start: 0.8268 (m-30) cc_final: 0.8021 (m-30) REVERT: A 1078 LYS cc_start: 0.8588 (tmtm) cc_final: 0.7933 (mtpp) REVERT: A 1124 LEU cc_start: 0.8119 (tp) cc_final: 0.7782 (tp) REVERT: A 1128 ASN cc_start: 0.8830 (t0) cc_final: 0.8333 (t0) REVERT: A 1175 MET cc_start: 0.8624 (tmm) cc_final: 0.8099 (tmm) REVERT: A 1269 LYS cc_start: 0.8218 (mttt) cc_final: 0.7935 (mtmp) REVERT: A 1308 VAL cc_start: 0.7768 (t) cc_final: 0.7161 (p) REVERT: A 1331 LYS cc_start: 0.6814 (tptm) cc_final: 0.6482 (ttmt) REVERT: A 1439 MET cc_start: 0.6583 (ppp) cc_final: 0.5811 (ptp) REVERT: A 1469 TRP cc_start: 0.6517 (p-90) cc_final: 0.6026 (p-90) REVERT: A 1475 GLU cc_start: 0.6861 (tt0) cc_final: 0.6172 (mt-10) REVERT: A 1483 LEU cc_start: 0.7386 (tt) cc_final: 0.6995 (tt) REVERT: A 1485 MET cc_start: 0.6360 (mmm) cc_final: 0.5413 (mmm) REVERT: A 1508 VAL cc_start: 0.7904 (t) cc_final: 0.7546 (m) REVERT: A 1634 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6719 (pp) REVERT: B 37 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8412 (tm) REVERT: B 54 GLU cc_start: 0.6899 (tt0) cc_final: 0.6561 (tp30) REVERT: B 90 TYR cc_start: 0.4939 (t80) cc_final: 0.4633 (t80) REVERT: B 188 ASP cc_start: 0.7610 (t70) cc_final: 0.7348 (t0) REVERT: B 243 GLN cc_start: 0.8612 (mp-120) cc_final: 0.8261 (mm-40) REVERT: B 311 ARG cc_start: 0.7113 (mpp80) cc_final: 0.6604 (mmm160) REVERT: B 317 TYR cc_start: 0.4912 (p90) cc_final: 0.4435 (p90) REVERT: B 336 VAL cc_start: 0.8682 (m) cc_final: 0.8457 (p) REVERT: B 389 CYS cc_start: 0.7751 (m) cc_final: 0.7465 (m) REVERT: B 420 TYR cc_start: 0.7254 (t80) cc_final: 0.6859 (t80) REVERT: B 434 ARG cc_start: 0.8498 (mmt90) cc_final: 0.7460 (ttt90) REVERT: B 446 MET cc_start: 0.6594 (tpp) cc_final: 0.6303 (tmm) REVERT: B 477 ASP cc_start: 0.6495 (t0) cc_final: 0.6230 (t0) REVERT: B 497 ILE cc_start: 0.8867 (tp) cc_final: 0.8583 (tp) REVERT: B 755 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8410 (m-40) REVERT: B 759 ASP cc_start: 0.8427 (t0) cc_final: 0.8036 (t0) REVERT: B 878 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8196 (tm-30) REVERT: B 915 ASP cc_start: 0.7219 (p0) cc_final: 0.7005 (p0) REVERT: B 946 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8620 (p0) REVERT: B 998 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8115 (pp20) REVERT: B 1020 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8010 (mm-30) REVERT: B 1039 MET cc_start: 0.6207 (pmt) cc_final: 0.5949 (pmm) REVERT: B 1089 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 1201 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7939 (tt0) REVERT: C 53 ASN cc_start: 0.7031 (t0) cc_final: 0.6743 (t0) REVERT: C 107 LYS cc_start: 0.7314 (mttt) cc_final: 0.6731 (tmmt) REVERT: C 237 GLN cc_start: 0.7825 (mt0) cc_final: 0.7404 (mm-40) REVERT: C 246 ARG cc_start: 0.6258 (ptp90) cc_final: 0.5893 (ptt180) REVERT: C 315 PHE cc_start: 0.7319 (t80) cc_final: 0.6894 (t80) REVERT: D 37 LEU cc_start: 0.6942 (mm) cc_final: 0.6466 (mp) REVERT: E 39 LEU cc_start: 0.6466 (tm) cc_final: 0.6034 (tm) REVERT: E 54 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7255 (mp10) REVERT: E 58 MET cc_start: 0.8620 (mtp) cc_final: 0.7776 (mtp) REVERT: E 132 ILE cc_start: 0.8097 (pt) cc_final: 0.7883 (tt) REVERT: E 142 VAL cc_start: 0.9203 (t) cc_final: 0.8758 (p) REVERT: E 143 ASN cc_start: 0.7934 (t160) cc_final: 0.7672 (t0) REVERT: E 145 THR cc_start: 0.8135 (m) cc_final: 0.7362 (p) REVERT: F 61 HIS cc_start: 0.7140 (m90) cc_final: 0.6926 (m-70) REVERT: F 67 LYS cc_start: 0.9027 (mtmp) cc_final: 0.8701 (mmmt) REVERT: F 99 LEU cc_start: 0.8826 (mt) cc_final: 0.8624 (mt) REVERT: F 144 GLU cc_start: 0.8570 (pp20) cc_final: 0.8080 (pp20) REVERT: G 62 MET cc_start: 0.8618 (mtm) cc_final: 0.8219 (mtp) REVERT: G 80 VAL cc_start: 0.8033 (t) cc_final: 0.7755 (p) REVERT: G 84 TYR cc_start: 0.6983 (p90) cc_final: 0.6760 (p90) REVERT: H 8 ASP cc_start: 0.7587 (t0) cc_final: 0.7307 (t70) REVERT: H 52 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7777 (pt0) REVERT: H 58 THR cc_start: 0.7925 (m) cc_final: 0.7122 (m) REVERT: H 87 ARG cc_start: 0.7182 (tmt170) cc_final: 0.6909 (mmt-90) REVERT: I 19 ASN cc_start: 0.4846 (OUTLIER) cc_final: 0.4105 (m110) REVERT: J 27 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8141 (mt-10) REVERT: J 55 ASP cc_start: 0.8994 (t70) cc_final: 0.8575 (t0) REVERT: K 44 ARG cc_start: 0.5787 (mmp-170) cc_final: 0.4923 (mpp-170) REVERT: K 55 SER cc_start: 0.7523 (t) cc_final: 0.6436 (p) REVERT: K 98 GLU cc_start: 0.7116 (pp20) cc_final: 0.6662 (pp20) REVERT: L 30 ILE cc_start: 0.8475 (pp) cc_final: 0.7905 (mm) REVERT: L 68 GLU cc_start: 0.7969 (tp30) cc_final: 0.6851 (mt-10) REVERT: N 33 LYS cc_start: 0.6448 (pmmt) cc_final: 0.5682 (mmtt) REVERT: N 88 LYS cc_start: 0.6147 (tttp) cc_final: 0.5727 (tppt) outliers start: 51 outliers final: 4 residues processed: 1116 average time/residue: 0.5130 time to fit residues: 899.1493 Evaluate side-chains 655 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 645 time to evaluate : 4.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 755 ASN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain I residue 19 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 358 optimal weight: 1.9990 chunk 321 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 332 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 202 optimal weight: 10.0000 chunk 247 optimal weight: 0.5980 chunk 385 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 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 785 GLN A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1072 ASN A1141 GLN A1250 GLN A1453 HIS 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 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 53 ASN C 99 HIS C 207 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 49 ASN D 88 GLN E 143 ASN E 146 HIS F 59 GLN G 59 GLN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS H 33 GLN H 43 ASN I 19 ASN J 53 HIS ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 35538 Z= 0.217 Angle : 0.642 17.390 48194 Z= 0.324 Chirality : 0.044 0.203 5380 Planarity : 0.005 0.056 6085 Dihedral : 10.659 83.118 5121 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.30 % Favored : 94.68 % Rotamer: Outliers : 4.57 % Allowed : 15.40 % Favored : 80.03 % 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: -2.94 (0.12), residues: 4211 helix: -1.64 (0.13), residues: 1196 sheet: -1.84 (0.19), residues: 599 loop : -2.18 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 595 HIS 0.008 0.001 HIS B 532 PHE 0.020 0.002 PHE F 58 TYR 0.022 0.002 TYR B 494 ARG 0.008 0.001 ARG A 855 *********************** 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 872 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 699 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.8267 (tppt) cc_final: 0.7916 (ttpt) REVERT: A 199 ASP cc_start: 0.6653 (p0) cc_final: 0.6260 (p0) REVERT: A 225 LYS cc_start: 0.7554 (tptm) cc_final: 0.7345 (tmmt) REVERT: A 342 ARG cc_start: 0.9067 (mtp85) cc_final: 0.8787 (mtt90) REVERT: A 347 ARG cc_start: 0.7451 (mtt180) cc_final: 0.6608 (tmt170) REVERT: A 446 ARG cc_start: 0.4398 (OUTLIER) cc_final: 0.3469 (mmp-170) REVERT: A 492 THR cc_start: 0.7955 (t) cc_final: 0.7700 (t) REVERT: A 540 ASP cc_start: 0.8369 (t70) cc_final: 0.8073 (t0) REVERT: A 601 MET cc_start: 0.8631 (mmm) cc_final: 0.8400 (mtp) REVERT: A 633 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8510 (ttm) REVERT: A 977 MET cc_start: 0.8461 (tmm) cc_final: 0.8143 (tmm) REVERT: A 1020 GLN cc_start: 0.7925 (mt0) cc_final: 0.7440 (tt0) REVERT: A 1124 LEU cc_start: 0.8382 (tp) cc_final: 0.8085 (tp) REVERT: A 1175 MET cc_start: 0.8493 (tmm) cc_final: 0.8119 (tmm) REVERT: A 1288 ARG cc_start: 0.6099 (tpp-160) cc_final: 0.5889 (ttm110) REVERT: A 1293 HIS cc_start: 0.7156 (t-90) cc_final: 0.6783 (t-90) REVERT: A 1439 MET cc_start: 0.6738 (ppp) cc_final: 0.6035 (ptm) REVERT: A 1469 TRP cc_start: 0.6912 (p-90) cc_final: 0.6345 (p-90) REVERT: A 1485 MET cc_start: 0.6526 (mmm) cc_final: 0.5608 (mmm) REVERT: A 1520 VAL cc_start: 0.7559 (t) cc_final: 0.7344 (t) REVERT: A 1588 MET cc_start: 0.8616 (mmm) cc_final: 0.8383 (mmm) REVERT: A 1616 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: A 1634 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7391 (pp) REVERT: B 37 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8516 (tm) REVERT: B 188 ASP cc_start: 0.7753 (t70) cc_final: 0.7418 (t0) REVERT: B 243 GLN cc_start: 0.8342 (mp-120) cc_final: 0.7780 (mm-40) REVERT: B 290 ASP cc_start: 0.8403 (t0) cc_final: 0.7862 (m-30) REVERT: B 302 LEU cc_start: 0.8388 (mp) cc_final: 0.8158 (mt) REVERT: B 305 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6364 (tpp-160) REVERT: B 311 ARG cc_start: 0.7111 (mpp80) cc_final: 0.6643 (mmm160) REVERT: B 317 TYR cc_start: 0.4997 (p90) cc_final: 0.4482 (p90) REVERT: B 373 MET cc_start: 0.8119 (tpp) cc_final: 0.7621 (tpt) REVERT: B 389 CYS cc_start: 0.7961 (m) cc_final: 0.7694 (m) REVERT: B 434 ARG cc_start: 0.8244 (mmt90) cc_final: 0.7506 (ttp80) REVERT: B 446 MET cc_start: 0.6434 (tpp) cc_final: 0.5782 (tmm) REVERT: B 447 SER cc_start: 0.8212 (m) cc_final: 0.7852 (p) REVERT: B 450 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7297 (tt) REVERT: B 497 ILE cc_start: 0.8984 (tp) cc_final: 0.8726 (tp) REVERT: B 604 ILE cc_start: 0.8383 (mt) cc_final: 0.8095 (mt) REVERT: B 742 TYR cc_start: 0.8559 (m-80) cc_final: 0.8081 (m-80) REVERT: B 746 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7352 (p) REVERT: B 759 ASP cc_start: 0.8368 (t0) cc_final: 0.8113 (t0) REVERT: B 803 MET cc_start: 0.7574 (ttm) cc_final: 0.7154 (ttm) REVERT: B 878 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8255 (tm-30) REVERT: B 883 GLU cc_start: 0.8317 (tp30) cc_final: 0.8113 (tp30) REVERT: B 998 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8147 (pp20) REVERT: B 1020 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8181 (mm-30) REVERT: B 1192 MET cc_start: 0.7655 (ptp) cc_final: 0.7434 (ptt) REVERT: C 53 ASN cc_start: 0.7422 (t0) cc_final: 0.7083 (t0) REVERT: C 107 LYS cc_start: 0.7497 (mttt) cc_final: 0.6785 (tmmt) REVERT: C 237 GLN cc_start: 0.7879 (mt0) cc_final: 0.7572 (mm-40) REVERT: C 315 PHE cc_start: 0.7458 (t80) cc_final: 0.6993 (t80) REVERT: E 50 MET cc_start: 0.6379 (tmm) cc_final: 0.6028 (tmm) REVERT: E 54 GLN cc_start: 0.8095 (tp-100) cc_final: 0.7157 (mp10) REVERT: E 58 MET cc_start: 0.8457 (mtp) cc_final: 0.8089 (mtp) REVERT: F 58 PHE cc_start: 0.6107 (t80) cc_final: 0.5779 (t80) REVERT: F 60 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8400 (mt0) REVERT: F 61 HIS cc_start: 0.7287 (m90) cc_final: 0.6808 (m-70) REVERT: F 144 GLU cc_start: 0.8554 (pp20) cc_final: 0.8297 (pp20) REVERT: G 62 MET cc_start: 0.8724 (mtm) cc_final: 0.8168 (mtm) REVERT: G 80 VAL cc_start: 0.8149 (t) cc_final: 0.7829 (p) REVERT: G 84 TYR cc_start: 0.7138 (p90) cc_final: 0.6576 (p90) REVERT: G 125 TRP cc_start: 0.7272 (t60) cc_final: 0.6794 (t60) REVERT: G 134 GLU cc_start: 0.2703 (OUTLIER) cc_final: 0.2378 (tm-30) REVERT: H 8 ASP cc_start: 0.7524 (t0) cc_final: 0.7303 (t70) REVERT: H 62 SER cc_start: 0.8717 (t) cc_final: 0.8324 (m) REVERT: H 87 ARG cc_start: 0.6977 (tmt170) cc_final: 0.6494 (mpt180) REVERT: H 89 LEU cc_start: 0.8418 (mt) cc_final: 0.7809 (tt) REVERT: I 54 ASP cc_start: 0.6556 (t0) cc_final: 0.6292 (t0) REVERT: J 55 ASP cc_start: 0.9001 (t70) cc_final: 0.8741 (t70) REVERT: K 44 ARG cc_start: 0.5974 (mmp-170) cc_final: 0.4966 (mpp-170) REVERT: K 56 GLU cc_start: 0.6571 (tp30) cc_final: 0.6347 (tp30) REVERT: K 98 GLU cc_start: 0.7265 (pp20) cc_final: 0.6645 (pp20) REVERT: L 29 TYR cc_start: 0.7449 (m-80) cc_final: 0.7224 (m-80) REVERT: L 30 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8231 (mp) REVERT: L 68 GLU cc_start: 0.8070 (tp30) cc_final: 0.6953 (mt-10) REVERT: M 43 LYS cc_start: 0.5637 (tptp) cc_final: 0.5353 (tppt) REVERT: N 33 LYS cc_start: 0.6341 (pmmt) cc_final: 0.5724 (mmtt) outliers start: 173 outliers final: 73 residues processed: 832 average time/residue: 0.4684 time to fit residues: 628.2708 Evaluate side-chains 668 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 585 time to evaluate : 4.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1453 HIS Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1571 SER Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1616 GLU Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain N residue 67 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 213 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 320 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 385 optimal weight: 7.9990 chunk 416 optimal weight: 30.0000 chunk 343 optimal weight: 1.9990 chunk 382 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 309 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** 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** A1250 GLN ** A1438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** 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 669 GLN B 764 ASN ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN C 137 ASN C 161 HIS C 216 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 35538 Z= 0.380 Angle : 0.734 17.388 48194 Z= 0.377 Chirality : 0.048 0.219 5380 Planarity : 0.006 0.071 6085 Dihedral : 10.878 81.481 5113 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.89 % Favored : 93.04 % Rotamer: Outliers : 5.60 % Allowed : 16.41 % Favored : 77.99 % 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: -2.66 (0.12), residues: 4211 helix: -1.17 (0.14), residues: 1214 sheet: -1.82 (0.19), residues: 588 loop : -2.11 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 595 HIS 0.017 0.002 HIS J 53 PHE 0.022 0.002 PHE C 300 TYR 0.031 0.003 TYR B 717 ARG 0.023 0.001 ARG B 305 *********************** 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 821 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 609 time to evaluate : 3.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8180 (pttp) cc_final: 0.7628 (pttm) REVERT: A 182 LYS cc_start: 0.8373 (tppt) cc_final: 0.8104 (ttmt) REVERT: A 201 ARG cc_start: 0.6749 (ttm110) cc_final: 0.5981 (mmm160) REVERT: A 225 LYS cc_start: 0.7611 (tptm) cc_final: 0.7297 (tmmt) REVERT: A 347 ARG cc_start: 0.7480 (mtt180) cc_final: 0.6785 (tmt170) REVERT: A 446 ARG cc_start: 0.3905 (OUTLIER) cc_final: 0.3225 (mmm160) REVERT: A 492 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8483 (t) REVERT: A 540 ASP cc_start: 0.8193 (t70) cc_final: 0.7880 (t0) REVERT: A 672 ASP cc_start: 0.8119 (m-30) cc_final: 0.7705 (m-30) REVERT: A 925 MET cc_start: 0.8004 (tmm) cc_final: 0.7440 (tmm) REVERT: A 1020 GLN cc_start: 0.8076 (mt0) cc_final: 0.7275 (tt0) REVERT: A 1175 MET cc_start: 0.8309 (tmm) cc_final: 0.7928 (tmm) REVERT: A 1439 MET cc_start: 0.6726 (ppp) cc_final: 0.6453 (ptm) REVERT: A 1440 ASN cc_start: 0.5911 (t0) cc_final: 0.5685 (t0) REVERT: A 1573 TYR cc_start: 0.5235 (OUTLIER) cc_final: 0.4479 (t80) REVERT: A 1588 MET cc_start: 0.8884 (mmm) cc_final: 0.8447 (mmm) REVERT: A 1634 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7668 (pp) REVERT: B 37 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8745 (tm) REVERT: B 290 ASP cc_start: 0.8253 (t0) cc_final: 0.7723 (m-30) REVERT: B 317 TYR cc_start: 0.5280 (p90) cc_final: 0.4189 (p90) REVERT: B 370 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7391 (mtpp) REVERT: B 389 CYS cc_start: 0.8188 (m) cc_final: 0.7914 (m) REVERT: B 434 ARG cc_start: 0.8266 (mmt90) cc_final: 0.7551 (tpt90) REVERT: B 447 SER cc_start: 0.8290 (m) cc_final: 0.7776 (p) REVERT: B 450 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7423 (tt) REVERT: B 497 ILE cc_start: 0.9173 (tp) cc_final: 0.8908 (tp) REVERT: B 502 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8201 (tmm) REVERT: B 576 THR cc_start: 0.5504 (OUTLIER) cc_final: 0.4979 (p) REVERT: B 595 TRP cc_start: 0.7472 (m100) cc_final: 0.7195 (m100) REVERT: B 677 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8102 (p) REVERT: B 700 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9055 (tt) REVERT: B 726 MET cc_start: 0.8388 (ttm) cc_final: 0.8070 (ttm) REVERT: B 746 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7748 (p) REVERT: B 760 TYR cc_start: 0.8895 (m-80) cc_final: 0.8320 (m-80) REVERT: B 854 GLU cc_start: 0.7950 (tt0) cc_final: 0.7709 (tm-30) REVERT: B 878 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8339 (tm-30) REVERT: B 883 GLU cc_start: 0.8235 (tp30) cc_final: 0.8028 (tp30) REVERT: B 967 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7386 (mp) REVERT: B 1002 LYS cc_start: 0.7716 (ptpt) cc_final: 0.7263 (mmtt) REVERT: B 1013 MET cc_start: 0.9007 (mtp) cc_final: 0.8052 (mtp) REVERT: B 1020 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8236 (mm-30) REVERT: B 1089 GLN cc_start: 0.8746 (tm-30) cc_final: 0.7968 (tm-30) REVERT: C 60 ASP cc_start: 0.7906 (t70) cc_final: 0.7656 (t0) REVERT: C 82 TYR cc_start: 0.8552 (m-80) cc_final: 0.8320 (m-80) REVERT: C 89 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8858 (p) REVERT: C 237 GLN cc_start: 0.7977 (mt0) cc_final: 0.7549 (mm-40) REVERT: C 308 MET cc_start: 0.7300 (mmt) cc_final: 0.7068 (mmt) REVERT: E 54 GLN cc_start: 0.8180 (tp-100) cc_final: 0.7174 (mp10) REVERT: E 146 HIS cc_start: 0.8230 (OUTLIER) cc_final: 0.7883 (m90) REVERT: E 164 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8129 (tp) REVERT: E 174 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: F 60 GLN cc_start: 0.9099 (tp-100) cc_final: 0.8401 (mt0) REVERT: F 61 HIS cc_start: 0.7196 (m90) cc_final: 0.6939 (m-70) REVERT: F 79 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7058 (ptt90) REVERT: F 144 GLU cc_start: 0.8616 (pp20) cc_final: 0.8198 (pp20) REVERT: F 150 GLU cc_start: 0.8751 (pt0) cc_final: 0.8407 (pt0) REVERT: G 76 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7338 (mmmt) REVERT: G 80 VAL cc_start: 0.8376 (t) cc_final: 0.8079 (p) REVERT: G 125 TRP cc_start: 0.7376 (t60) cc_final: 0.6812 (t60) REVERT: H 8 ASP cc_start: 0.7468 (t0) cc_final: 0.7214 (t0) REVERT: H 14 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8072 (tm-30) REVERT: H 87 ARG cc_start: 0.7063 (tmt170) cc_final: 0.6473 (mmt-90) REVERT: H 89 LEU cc_start: 0.8632 (mt) cc_final: 0.7954 (tt) REVERT: H 97 MET cc_start: 0.8006 (mtm) cc_final: 0.7779 (mtm) REVERT: I 54 ASP cc_start: 0.6420 (t0) cc_final: 0.6049 (t0) REVERT: K 44 ARG cc_start: 0.6292 (mmp-170) cc_final: 0.5093 (mpp-170) REVERT: K 98 GLU cc_start: 0.7275 (pp20) cc_final: 0.6636 (pp20) REVERT: K 110 GLU cc_start: 0.8585 (pt0) cc_final: 0.7947 (pp20) REVERT: L 29 TYR cc_start: 0.7583 (m-80) cc_final: 0.7339 (m-80) REVERT: L 30 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8364 (mp) REVERT: L 54 ARG cc_start: 0.6774 (mtp85) cc_final: 0.6560 (mmm-85) REVERT: M 60 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5737 (tm) REVERT: N 33 LYS cc_start: 0.6585 (pmmt) cc_final: 0.5899 (mmtt) outliers start: 212 outliers final: 114 residues processed: 775 average time/residue: 0.4593 time to fit residues: 581.4627 Evaluate side-chains 675 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 541 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1571 SER Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 69 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 381 optimal weight: 2.9990 chunk 290 optimal weight: 7.9990 chunk 200 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 chunk 387 optimal weight: 5.9990 chunk 409 optimal weight: 30.0000 chunk 202 optimal weight: 2.9990 chunk 366 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 213 ASN A 221 HIS A 515 ASN ** 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 A1293 HIS ** 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 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.3876 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= 0.243 Angle : 0.647 18.220 48194 Z= 0.325 Chirality : 0.045 0.223 5380 Planarity : 0.004 0.055 6085 Dihedral : 10.777 81.579 5113 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.06 % Favored : 93.92 % Rotamer: Outliers : 4.86 % Allowed : 18.44 % Favored : 76.70 % 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: -2.33 (0.12), residues: 4211 helix: -0.79 (0.14), residues: 1215 sheet: -1.70 (0.20), residues: 594 loop : -1.94 (0.12), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 525 HIS 0.011 0.001 HIS J 53 PHE 0.024 0.002 PHE A1296 TYR 0.022 0.002 TYR E 28 ARG 0.009 0.001 ARG G 40 *********************** 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 768 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 584 time to evaluate : 4.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8075 (pttp) cc_final: 0.7367 (pttm) REVERT: A 182 LYS cc_start: 0.8368 (tppt) cc_final: 0.8136 (ttmt) REVERT: A 213 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.8038 (m110) REVERT: A 347 ARG cc_start: 0.7534 (mtt180) cc_final: 0.6699 (tmt170) REVERT: A 446 ARG cc_start: 0.3645 (OUTLIER) cc_final: 0.3149 (mmm160) REVERT: A 543 LEU cc_start: 0.7679 (tp) cc_final: 0.7406 (mp) REVERT: A 925 MET cc_start: 0.8015 (tmm) cc_final: 0.7420 (tmm) REVERT: A 977 MET cc_start: 0.8481 (tmm) cc_final: 0.7823 (tmm) REVERT: A 1020 GLN cc_start: 0.7959 (mt0) cc_final: 0.7163 (tt0) REVERT: A 1175 MET cc_start: 0.8359 (tmm) cc_final: 0.8107 (tmm) REVERT: A 1227 MET cc_start: 0.7784 (mmm) cc_final: 0.6664 (mmm) REVERT: A 1440 ASN cc_start: 0.5901 (t0) cc_final: 0.5650 (t0) REVERT: A 1573 TYR cc_start: 0.5251 (OUTLIER) cc_final: 0.4572 (t80) REVERT: A 1588 MET cc_start: 0.8939 (mmm) cc_final: 0.8126 (tpt) REVERT: A 1634 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7693 (pp) REVERT: B 37 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8684 (tm) REVERT: B 205 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7588 (mtt) REVERT: B 243 GLN cc_start: 0.8556 (mp-120) cc_final: 0.8108 (mm-40) REVERT: B 305 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.5677 (tpp-160) REVERT: B 308 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7131 (mm) REVERT: B 317 TYR cc_start: 0.5254 (p90) cc_final: 0.4002 (p90) REVERT: B 335 ARG cc_start: 0.6863 (tpt170) cc_final: 0.6451 (tpp-160) REVERT: B 346 ASP cc_start: 0.7628 (p0) cc_final: 0.6446 (p0) REVERT: B 370 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7501 (mtpp) REVERT: B 389 CYS cc_start: 0.8232 (m) cc_final: 0.7991 (m) REVERT: B 434 ARG cc_start: 0.8303 (mmt90) cc_final: 0.7254 (tpt90) REVERT: B 446 MET cc_start: 0.6477 (tpp) cc_final: 0.5785 (tmm) REVERT: B 447 SER cc_start: 0.8220 (m) cc_final: 0.7874 (p) REVERT: B 450 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7395 (tt) REVERT: B 497 ILE cc_start: 0.9190 (tp) cc_final: 0.8949 (tp) REVERT: B 502 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8113 (tmm) REVERT: B 677 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.7969 (p) REVERT: B 700 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9121 (tt) REVERT: B 726 MET cc_start: 0.8374 (ttm) cc_final: 0.8135 (ttm) REVERT: B 742 TYR cc_start: 0.8984 (m-80) cc_final: 0.8352 (m-10) REVERT: B 746 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7646 (p) REVERT: B 1002 LYS cc_start: 0.7741 (ptpt) cc_final: 0.7343 (mmtt) REVERT: B 1013 MET cc_start: 0.9011 (mtp) cc_final: 0.8291 (mtp) REVERT: B 1020 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8223 (mm-30) REVERT: B 1089 GLN cc_start: 0.8669 (tm-30) cc_final: 0.7854 (tm-30) REVERT: C 60 ASP cc_start: 0.7913 (t70) cc_final: 0.7623 (t0) REVERT: C 63 ILE cc_start: 0.8603 (mm) cc_final: 0.8219 (mt) REVERT: C 82 TYR cc_start: 0.8592 (m-80) cc_final: 0.8326 (m-80) REVERT: C 89 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8998 (p) REVERT: C 237 GLN cc_start: 0.7944 (mt0) cc_final: 0.7517 (mm-40) REVERT: E 50 MET cc_start: 0.7173 (tmm) cc_final: 0.6777 (ppp) REVERT: E 54 GLN cc_start: 0.8178 (tp-100) cc_final: 0.7296 (mp10) REVERT: E 58 MET cc_start: 0.8506 (mtp) cc_final: 0.8149 (mtp) REVERT: E 78 LEU cc_start: 0.8465 (pp) cc_final: 0.8218 (pp) REVERT: E 146 HIS cc_start: 0.8030 (OUTLIER) cc_final: 0.7829 (m90) REVERT: F 60 GLN cc_start: 0.9024 (tp-100) cc_final: 0.8374 (mt0) REVERT: F 61 HIS cc_start: 0.7207 (m90) cc_final: 0.6668 (m-70) REVERT: F 144 GLU cc_start: 0.8458 (pp20) cc_final: 0.8189 (pp20) REVERT: F 150 GLU cc_start: 0.8769 (pt0) cc_final: 0.8497 (pt0) REVERT: G 80 VAL cc_start: 0.8303 (t) cc_final: 0.8064 (p) REVERT: G 125 TRP cc_start: 0.7277 (t60) cc_final: 0.6799 (t60) REVERT: H 62 SER cc_start: 0.8788 (t) cc_final: 0.8380 (m) REVERT: H 87 ARG cc_start: 0.6982 (tmt170) cc_final: 0.6385 (mmt-90) REVERT: H 89 LEU cc_start: 0.8438 (mt) cc_final: 0.7852 (tt) REVERT: I 7 LEU cc_start: 0.7367 (mt) cc_final: 0.7039 (mt) REVERT: I 54 ASP cc_start: 0.6368 (t0) cc_final: 0.5963 (t0) REVERT: I 66 VAL cc_start: 0.5143 (OUTLIER) cc_final: 0.4899 (p) REVERT: J 30 LEU cc_start: 0.6911 (mt) cc_final: 0.6695 (mp) REVERT: K 44 ARG cc_start: 0.6285 (mmp-170) cc_final: 0.5196 (mpp-170) REVERT: K 98 GLU cc_start: 0.7068 (pp20) cc_final: 0.6466 (pp20) REVERT: L 30 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8464 (mp) REVERT: M 60 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5747 (tm) REVERT: N 33 LYS cc_start: 0.6542 (pmmt) cc_final: 0.5877 (mmtt) outliers start: 184 outliers final: 98 residues processed: 723 average time/residue: 0.4545 time to fit residues: 539.2710 Evaluate side-chains 665 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 548 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 107 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 341 optimal weight: 0.9990 chunk 232 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 305 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 349 optimal weight: 40.0000 chunk 283 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 367 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS A 378 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** ** A1108 HIS ** 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 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN N 106 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35538 Z= 0.227 Angle : 0.633 18.127 48194 Z= 0.318 Chirality : 0.044 0.226 5380 Planarity : 0.004 0.054 6085 Dihedral : 10.717 80.973 5113 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 5.42 % Allowed : 18.81 % Favored : 75.77 % 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: -2.12 (0.12), residues: 4211 helix: -0.55 (0.15), residues: 1222 sheet: -1.57 (0.20), residues: 592 loop : -1.86 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 595 HIS 0.009 0.001 HIS J 53 PHE 0.021 0.001 PHE A 223 TYR 0.020 0.002 TYR B 420 ARG 0.006 0.000 ARG F 92 *********************** 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 767 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 562 time to evaluate : 3.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8143 (pttp) cc_final: 0.7470 (pttm) REVERT: A 347 ARG cc_start: 0.7542 (mtt180) cc_final: 0.6689 (tmt170) REVERT: A 446 ARG cc_start: 0.3655 (OUTLIER) cc_final: 0.3222 (mmm160) REVERT: A 543 LEU cc_start: 0.7637 (tp) cc_final: 0.7423 (mp) REVERT: A 925 MET cc_start: 0.8137 (tmm) cc_final: 0.7472 (tmm) REVERT: A 977 MET cc_start: 0.8485 (tmm) cc_final: 0.7785 (tmm) REVERT: A 1020 GLN cc_start: 0.7973 (mt0) cc_final: 0.7199 (tt0) REVERT: A 1064 THR cc_start: 0.7264 (OUTLIER) cc_final: 0.7040 (m) REVERT: A 1085 LEU cc_start: 0.8401 (mt) cc_final: 0.7703 (tt) REVERT: A 1124 LEU cc_start: 0.8784 (tp) cc_final: 0.8565 (mt) REVERT: A 1175 MET cc_start: 0.8364 (tmm) cc_final: 0.8147 (tmm) REVERT: A 1227 MET cc_start: 0.7766 (mmm) cc_final: 0.6797 (mmm) REVERT: A 1334 LYS cc_start: 0.8312 (mtmm) cc_final: 0.7910 (ttpt) REVERT: A 1573 TYR cc_start: 0.5326 (OUTLIER) cc_final: 0.4641 (t80) REVERT: A 1588 MET cc_start: 0.8964 (mmm) cc_final: 0.8160 (tpt) REVERT: A 1634 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7760 (pp) REVERT: B 37 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8689 (tm) REVERT: B 205 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7668 (tpp) REVERT: B 243 GLN cc_start: 0.8645 (mp-120) cc_final: 0.8146 (mm-40) REVERT: B 286 ARG cc_start: 0.6796 (tpm170) cc_final: 0.5926 (tpm170) REVERT: B 305 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.5618 (tpp-160) REVERT: B 308 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7077 (mm) REVERT: B 317 TYR cc_start: 0.5294 (p90) cc_final: 0.3902 (p90) REVERT: B 335 ARG cc_start: 0.6864 (tpt170) cc_final: 0.6526 (tpp-160) REVERT: B 370 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7385 (mtpp) REVERT: B 373 MET cc_start: 0.7872 (tpp) cc_final: 0.7560 (tpp) REVERT: B 389 CYS cc_start: 0.8241 (m) cc_final: 0.7997 (m) REVERT: B 434 ARG cc_start: 0.8303 (mmt90) cc_final: 0.7490 (tpt90) REVERT: B 446 MET cc_start: 0.6655 (tpp) cc_final: 0.5976 (tmm) REVERT: B 447 SER cc_start: 0.7812 (m) cc_final: 0.7085 (p) REVERT: B 497 ILE cc_start: 0.9196 (tp) cc_final: 0.8972 (tp) REVERT: B 502 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8220 (tmm) REVERT: B 668 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7450 (mm-30) REVERT: B 677 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7614 (p) REVERT: B 700 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9125 (tt) REVERT: B 746 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7628 (p) REVERT: B 967 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7483 (mp) REVERT: B 1002 LYS cc_start: 0.7737 (ptpt) cc_final: 0.7344 (mmtt) REVERT: B 1013 MET cc_start: 0.8974 (mtp) cc_final: 0.8275 (mtp) REVERT: B 1089 GLN cc_start: 0.8559 (tm-30) cc_final: 0.7765 (tm-30) REVERT: C 60 ASP cc_start: 0.7853 (t70) cc_final: 0.7577 (t0) REVERT: C 63 ILE cc_start: 0.8597 (mm) cc_final: 0.8204 (mt) REVERT: C 82 TYR cc_start: 0.8620 (m-80) cc_final: 0.8198 (m-80) REVERT: C 89 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8991 (p) REVERT: C 237 GLN cc_start: 0.7944 (mt0) cc_final: 0.7502 (mm-40) REVERT: E 54 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7329 (mp10) REVERT: E 58 MET cc_start: 0.8534 (mtp) cc_final: 0.8058 (mtp) REVERT: E 78 LEU cc_start: 0.8793 (pp) cc_final: 0.8563 (pp) REVERT: E 164 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8119 (tp) REVERT: F 60 GLN cc_start: 0.9059 (tp-100) cc_final: 0.8452 (mt0) REVERT: F 61 HIS cc_start: 0.7717 (m90) cc_final: 0.7107 (m-70) REVERT: F 79 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6914 (ptt90) REVERT: F 144 GLU cc_start: 0.8389 (pp20) cc_final: 0.8076 (pp20) REVERT: F 150 GLU cc_start: 0.8778 (pt0) cc_final: 0.8486 (pt0) REVERT: G 80 VAL cc_start: 0.8276 (t) cc_final: 0.7981 (p) REVERT: G 125 TRP cc_start: 0.7171 (t60) cc_final: 0.6675 (t60) REVERT: H 87 ARG cc_start: 0.6954 (tmt170) cc_final: 0.6392 (mmt-90) REVERT: H 89 LEU cc_start: 0.8488 (mt) cc_final: 0.7864 (tt) REVERT: I 7 LEU cc_start: 0.7452 (mt) cc_final: 0.7158 (mt) REVERT: I 54 ASP cc_start: 0.6396 (t0) cc_final: 0.6014 (t0) REVERT: I 66 VAL cc_start: 0.5173 (OUTLIER) cc_final: 0.4941 (p) REVERT: K 44 ARG cc_start: 0.6351 (mmp-170) cc_final: 0.5182 (mpp-170) REVERT: K 125 MET cc_start: 0.7438 (mmt) cc_final: 0.7208 (mmp) REVERT: L 30 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8474 (mp) REVERT: M 60 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5746 (tm) REVERT: M 90 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.6706 (mm) REVERT: N 33 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.5876 (mmtt) outliers start: 205 outliers final: 115 residues processed: 707 average time/residue: 0.4477 time to fit residues: 519.1779 Evaluate side-chains 667 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 530 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 106 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 137 optimal weight: 7.9990 chunk 369 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 240 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 410 optimal weight: 0.0570 chunk 340 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 221 HIS ** A 535 GLN ** 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 ** 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 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** C 301 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** N 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35538 Z= 0.286 Angle : 0.656 14.384 48194 Z= 0.333 Chirality : 0.045 0.188 5380 Planarity : 0.004 0.056 6085 Dihedral : 10.743 80.254 5111 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.70 % Favored : 93.28 % Rotamer: Outliers : 5.36 % Allowed : 18.89 % Favored : 75.75 % 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: -2.09 (0.12), residues: 4211 helix: -0.53 (0.15), residues: 1227 sheet: -1.53 (0.21), residues: 574 loop : -1.85 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 525 HIS 0.017 0.001 HIS A 221 PHE 0.018 0.001 PHE A 223 TYR 0.020 0.002 TYR B 420 ARG 0.007 0.001 ARG B 448 *********************** 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 753 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 550 time to evaluate : 3.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8159 (pttp) cc_final: 0.7487 (pttm) REVERT: A 347 ARG cc_start: 0.7598 (mtt180) cc_final: 0.6797 (tmt170) REVERT: A 433 ASP cc_start: 0.7360 (t0) cc_final: 0.7145 (t0) REVERT: A 446 ARG cc_start: 0.3712 (OUTLIER) cc_final: 0.3311 (mmm160) REVERT: A 835 LEU cc_start: 0.8208 (pp) cc_final: 0.7841 (pp) REVERT: A 925 MET cc_start: 0.8140 (tmm) cc_final: 0.7503 (tmm) REVERT: A 977 MET cc_start: 0.8470 (tmm) cc_final: 0.7998 (tmm) REVERT: A 1020 GLN cc_start: 0.8000 (mt0) cc_final: 0.7168 (tt0) REVERT: A 1085 LEU cc_start: 0.8522 (mt) cc_final: 0.7819 (tt) REVERT: A 1175 MET cc_start: 0.8333 (tmm) cc_final: 0.8089 (tmm) REVERT: A 1227 MET cc_start: 0.7815 (mmm) cc_final: 0.6773 (mmm) REVERT: A 1334 LYS cc_start: 0.8362 (mtmm) cc_final: 0.8011 (ttpt) REVERT: A 1573 TYR cc_start: 0.5273 (OUTLIER) cc_final: 0.4550 (t80) REVERT: A 1588 MET cc_start: 0.9056 (mmm) cc_final: 0.8311 (tpt) REVERT: A 1599 ASN cc_start: 0.6885 (p0) cc_final: 0.6486 (p0) REVERT: A 1634 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7801 (pp) REVERT: B 37 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8459 (tm) REVERT: B 128 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7283 (mp10) REVERT: B 205 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7678 (mtt) REVERT: B 290 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: B 305 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.5671 (tpp-160) REVERT: B 308 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7053 (mm) REVERT: B 373 MET cc_start: 0.8080 (tpp) cc_final: 0.7708 (tpp) REVERT: B 389 CYS cc_start: 0.8226 (m) cc_final: 0.8012 (m) REVERT: B 434 ARG cc_start: 0.8342 (mmt90) cc_final: 0.7507 (tpt90) REVERT: B 446 MET cc_start: 0.6569 (tpp) cc_final: 0.5659 (tmm) REVERT: B 502 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8252 (tmm) REVERT: B 668 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7402 (mm-30) REVERT: B 700 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9207 (tt) REVERT: B 723 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7820 (mtmm) REVERT: B 746 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7700 (p) REVERT: B 783 MET cc_start: 0.6292 (mmp) cc_final: 0.5937 (mmp) REVERT: B 967 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7500 (mp) REVERT: B 1002 LYS cc_start: 0.7758 (ptpt) cc_final: 0.7331 (mmtt) REVERT: B 1013 MET cc_start: 0.8946 (mtp) cc_final: 0.8260 (mtp) REVERT: B 1089 GLN cc_start: 0.8587 (tm-30) cc_final: 0.7806 (tm-30) REVERT: C 60 ASP cc_start: 0.7967 (t70) cc_final: 0.7687 (t0) REVERT: C 63 ILE cc_start: 0.8570 (mm) cc_final: 0.8180 (mt) REVERT: C 74 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7942 (tp30) REVERT: C 82 TYR cc_start: 0.8695 (m-80) cc_final: 0.8126 (m-80) REVERT: C 89 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8984 (p) REVERT: C 93 GLN cc_start: 0.8417 (mp10) cc_final: 0.8063 (mp10) REVERT: C 237 GLN cc_start: 0.7945 (mt0) cc_final: 0.7507 (mm-40) REVERT: E 54 GLN cc_start: 0.8284 (tp-100) cc_final: 0.7341 (mp10) REVERT: E 58 MET cc_start: 0.8597 (mtp) cc_final: 0.8109 (mtp) REVERT: E 78 LEU cc_start: 0.8953 (pp) cc_final: 0.8737 (pp) REVERT: E 164 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8008 (tp) REVERT: F 60 GLN cc_start: 0.9061 (tp-100) cc_final: 0.8437 (mt0) REVERT: F 61 HIS cc_start: 0.7678 (m90) cc_final: 0.7067 (m-70) REVERT: F 79 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6969 (ptt90) REVERT: F 144 GLU cc_start: 0.8345 (pp20) cc_final: 0.7992 (pp20) REVERT: F 150 GLU cc_start: 0.8865 (pt0) cc_final: 0.8583 (pt0) REVERT: G 125 TRP cc_start: 0.7246 (t60) cc_final: 0.6762 (t60) REVERT: H 87 ARG cc_start: 0.6952 (tmt170) cc_final: 0.6372 (mmt-90) REVERT: H 89 LEU cc_start: 0.8610 (mt) cc_final: 0.7919 (tt) REVERT: I 54 ASP cc_start: 0.6336 (t0) cc_final: 0.5951 (t0) REVERT: I 66 VAL cc_start: 0.5252 (OUTLIER) cc_final: 0.5011 (p) REVERT: J 28 ASP cc_start: 0.8214 (m-30) cc_final: 0.7977 (m-30) REVERT: K 44 ARG cc_start: 0.6434 (mmp-170) cc_final: 0.5242 (mpp-170) REVERT: K 125 MET cc_start: 0.7375 (mmt) cc_final: 0.7144 (mmp) REVERT: L 30 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8476 (mp) REVERT: M 90 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.6811 (mm) REVERT: N 33 LYS cc_start: 0.6170 (pmmt) cc_final: 0.5653 (mmtt) outliers start: 203 outliers final: 142 residues processed: 698 average time/residue: 0.4487 time to fit residues: 517.5967 Evaluate side-chains 692 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 529 time to evaluate : 3.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 34 LYS Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 51 PHE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 395 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 233 optimal weight: 0.0050 chunk 299 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 345 optimal weight: 40.0000 chunk 229 optimal weight: 3.9990 chunk 408 optimal weight: 0.0070 chunk 255 optimal weight: 0.8980 chunk 249 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 overall best weight: 0.7014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** 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** A1453 HIS ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN C 161 HIS ** C 301 ASN ** 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** L 53 HIS N 106 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35538 Z= 0.170 Angle : 0.611 11.019 48194 Z= 0.306 Chirality : 0.043 0.204 5380 Planarity : 0.004 0.055 6085 Dihedral : 10.621 81.616 5111 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 4.10 % Allowed : 20.95 % Favored : 74.95 % 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: -1.77 (0.13), residues: 4211 helix: -0.16 (0.15), residues: 1208 sheet: -1.34 (0.21), residues: 580 loop : -1.70 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 525 HIS 0.020 0.001 HIS A 221 PHE 0.018 0.001 PHE A 223 TYR 0.017 0.001 TYR B 420 ARG 0.006 0.000 ARG A 342 *********************** 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 740 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 585 time to evaluate : 4.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8056 (pttp) cc_final: 0.7443 (pttm) REVERT: A 82 PRO cc_start: 0.8363 (Cg_endo) cc_final: 0.8099 (Cg_exo) REVERT: A 347 ARG cc_start: 0.7589 (mtt180) cc_final: 0.6664 (tmt170) REVERT: A 446 ARG cc_start: 0.3556 (OUTLIER) cc_final: 0.3225 (mmm160) REVERT: A 632 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 799 GLU cc_start: 0.8680 (tp30) cc_final: 0.8431 (tp30) REVERT: A 835 LEU cc_start: 0.8094 (pp) cc_final: 0.7690 (pp) REVERT: A 925 MET cc_start: 0.8051 (tmm) cc_final: 0.7449 (tmm) REVERT: A 977 MET cc_start: 0.8416 (tmm) cc_final: 0.8088 (tmm) REVERT: A 1020 GLN cc_start: 0.7924 (mt0) cc_final: 0.7086 (tt0) REVERT: A 1064 THR cc_start: 0.6665 (OUTLIER) cc_final: 0.6407 (m) REVERT: A 1085 LEU cc_start: 0.8413 (mt) cc_final: 0.7861 (tt) REVERT: A 1175 MET cc_start: 0.8369 (tmm) cc_final: 0.8064 (tmm) REVERT: A 1227 MET cc_start: 0.7779 (mmm) cc_final: 0.6964 (mmm) REVERT: A 1334 LYS cc_start: 0.8357 (mtmm) cc_final: 0.8043 (ttpt) REVERT: A 1573 TYR cc_start: 0.4813 (OUTLIER) cc_final: 0.4196 (t80) REVERT: A 1588 MET cc_start: 0.9062 (mmm) cc_final: 0.8126 (tpt) REVERT: A 1632 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 1634 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7716 (pp) REVERT: B 37 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8729 (mm) REVERT: B 71 LYS cc_start: 0.7414 (mtpp) cc_final: 0.6637 (mmtt) REVERT: B 128 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7222 (mp10) REVERT: B 205 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7627 (tpp) REVERT: B 243 GLN cc_start: 0.8647 (mp-120) cc_final: 0.8226 (mm-40) REVERT: B 268 GLU cc_start: 0.8484 (pm20) cc_final: 0.7935 (tt0) REVERT: B 286 ARG cc_start: 0.6721 (tpm170) cc_final: 0.5947 (tpm170) REVERT: B 305 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.5683 (tpp-160) REVERT: B 373 MET cc_start: 0.8080 (tpp) cc_final: 0.7652 (tpp) REVERT: B 389 CYS cc_start: 0.8266 (m) cc_final: 0.8025 (m) REVERT: B 434 ARG cc_start: 0.8294 (mmt90) cc_final: 0.7442 (tpt90) REVERT: B 467 THR cc_start: 0.7142 (m) cc_final: 0.6827 (p) REVERT: B 480 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7916 (mp-120) REVERT: B 502 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8192 (tmm) REVERT: B 525 TRP cc_start: 0.8122 (t-100) cc_final: 0.7664 (t-100) REVERT: B 584 CYS cc_start: 0.7507 (p) cc_final: 0.7259 (p) REVERT: B 667 PHE cc_start: 0.8220 (t80) cc_final: 0.7359 (t80) REVERT: B 668 GLU cc_start: 0.7714 (mm-30) cc_final: 0.6445 (tp30) REVERT: B 726 MET cc_start: 0.8516 (ttm) cc_final: 0.8275 (ttm) REVERT: B 746 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7545 (p) REVERT: B 760 TYR cc_start: 0.8765 (m-80) cc_final: 0.8004 (m-80) REVERT: B 967 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7402 (mp) REVERT: B 1002 LYS cc_start: 0.7732 (ptpt) cc_final: 0.7252 (mmtt) REVERT: B 1013 MET cc_start: 0.8847 (mtp) cc_final: 0.8170 (mtp) REVERT: B 1037 ARG cc_start: 0.8302 (ttp80) cc_final: 0.8081 (ttp-170) REVERT: B 1089 GLN cc_start: 0.8444 (tm-30) cc_final: 0.7745 (tm-30) REVERT: C 63 ILE cc_start: 0.8576 (mm) cc_final: 0.8200 (mt) REVERT: C 74 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7954 (tp30) REVERT: C 82 TYR cc_start: 0.8638 (m-80) cc_final: 0.8243 (m-80) REVERT: C 89 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.8996 (p) REVERT: C 237 GLN cc_start: 0.7930 (mt0) cc_final: 0.7497 (mm-40) REVERT: D 38 GLN cc_start: 0.6507 (tp40) cc_final: 0.4912 (mt0) REVERT: E 21 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7663 (mt-10) REVERT: E 54 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7315 (mp10) REVERT: E 58 MET cc_start: 0.8581 (mtp) cc_final: 0.8001 (mtp) REVERT: E 113 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7753 (pt0) REVERT: E 164 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7870 (tp) REVERT: F 60 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8343 (mt0) REVERT: F 61 HIS cc_start: 0.7627 (m90) cc_final: 0.7351 (m-70) REVERT: F 79 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6984 (ptt90) REVERT: F 88 TYR cc_start: 0.8625 (m-80) cc_final: 0.8424 (m-80) REVERT: F 150 GLU cc_start: 0.8827 (pt0) cc_final: 0.8600 (pt0) REVERT: G 71 MET cc_start: 0.8081 (mmm) cc_final: 0.7649 (tpt) REVERT: G 125 TRP cc_start: 0.7184 (t60) cc_final: 0.6771 (t60) REVERT: H 52 GLN cc_start: 0.8497 (pm20) cc_final: 0.8296 (pm20) REVERT: H 62 SER cc_start: 0.8726 (t) cc_final: 0.8387 (m) REVERT: H 87 ARG cc_start: 0.6944 (tmt170) cc_final: 0.6602 (mmt-90) REVERT: H 89 LEU cc_start: 0.8549 (mt) cc_final: 0.7849 (tt) REVERT: I 54 ASP cc_start: 0.6722 (t0) cc_final: 0.6400 (t0) REVERT: K 44 ARG cc_start: 0.6435 (mmp-170) cc_final: 0.5267 (mpp-170) REVERT: K 52 GLN cc_start: 0.8828 (mp10) cc_final: 0.8094 (mt0) REVERT: K 81 MET cc_start: 0.9200 (mmm) cc_final: 0.8997 (mmt) REVERT: K 140 LYS cc_start: 0.7959 (tppt) cc_final: 0.7656 (ttpp) REVERT: L 30 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8423 (mp) REVERT: M 90 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.6832 (mm) REVERT: N 33 LYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5748 (mmtt) outliers start: 155 outliers final: 101 residues processed: 692 average time/residue: 0.4604 time to fit residues: 523.8131 Evaluate side-chains 652 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 531 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 831 ASP Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 34 LYS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 51 PHE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 252 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 259 optimal weight: 0.0870 chunk 278 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 321 optimal weight: 2.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 537 GLN ** A 592 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 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN B1114 GLN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 HIS ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 35538 Z= 0.275 Angle : 0.657 11.401 48194 Z= 0.332 Chirality : 0.045 0.280 5380 Planarity : 0.004 0.057 6085 Dihedral : 10.680 80.999 5111 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.65 % Favored : 93.33 % Rotamer: Outliers : 4.76 % Allowed : 20.61 % Favored : 74.64 % 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: -1.85 (0.12), residues: 4211 helix: -0.32 (0.15), residues: 1242 sheet: -1.39 (0.21), residues: 570 loop : -1.71 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 595 HIS 0.013 0.001 HIS J 53 PHE 0.019 0.001 PHE A 355 TYR 0.020 0.002 TYR A1615 ARG 0.005 0.001 ARG A1580 *********************** 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 715 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 535 time to evaluate : 3.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8203 (pttp) cc_final: 0.7545 (pttm) REVERT: A 347 ARG cc_start: 0.7590 (mtt180) cc_final: 0.6794 (tmt170) REVERT: A 433 ASP cc_start: 0.7337 (t0) cc_final: 0.7111 (t0) REVERT: A 446 ARG cc_start: 0.3720 (OUTLIER) cc_final: 0.3316 (mmm160) REVERT: A 472 MET cc_start: 0.8723 (mmp) cc_final: 0.8505 (mmp) REVERT: A 835 LEU cc_start: 0.8196 (pp) cc_final: 0.7814 (pp) REVERT: A 925 MET cc_start: 0.8076 (tmm) cc_final: 0.7468 (tmm) REVERT: A 928 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8277 (tmm) REVERT: A 1020 GLN cc_start: 0.8001 (mt0) cc_final: 0.7349 (tt0) REVERT: A 1064 THR cc_start: 0.6497 (OUTLIER) cc_final: 0.6266 (m) REVERT: A 1085 LEU cc_start: 0.8439 (mt) cc_final: 0.7819 (tt) REVERT: A 1175 MET cc_start: 0.8340 (tmm) cc_final: 0.8084 (tmm) REVERT: A 1227 MET cc_start: 0.7782 (mmm) cc_final: 0.7011 (mmm) REVERT: A 1464 ASP cc_start: 0.6990 (p0) cc_final: 0.6244 (m-30) REVERT: A 1573 TYR cc_start: 0.5154 (OUTLIER) cc_final: 0.4527 (t80) REVERT: A 1588 MET cc_start: 0.9067 (mmm) cc_final: 0.8286 (tpt) REVERT: A 1632 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 1634 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7765 (pp) REVERT: B 37 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8457 (tm) REVERT: B 71 LYS cc_start: 0.7521 (mtpp) cc_final: 0.6685 (mmtt) REVERT: B 128 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: B 164 MET cc_start: 0.7901 (ttm) cc_final: 0.7541 (ttp) REVERT: B 205 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7645 (mtt) REVERT: B 305 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.5772 (tpp-160) REVERT: B 308 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7146 (mm) REVERT: B 373 MET cc_start: 0.8049 (tpp) cc_final: 0.7644 (tpp) REVERT: B 389 CYS cc_start: 0.8291 (m) cc_final: 0.8086 (m) REVERT: B 434 ARG cc_start: 0.8295 (mmt90) cc_final: 0.7512 (tpt90) REVERT: B 467 THR cc_start: 0.7366 (m) cc_final: 0.7000 (p) REVERT: B 480 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8113 (mp-120) REVERT: B 502 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8255 (tmm) REVERT: B 606 ASP cc_start: 0.7992 (t0) cc_final: 0.7787 (t0) REVERT: B 667 PHE cc_start: 0.8351 (t80) cc_final: 0.7534 (t80) REVERT: B 668 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7393 (mm-30) REVERT: B 723 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7713 (mtmm) REVERT: B 726 MET cc_start: 0.8583 (ttm) cc_final: 0.8319 (ttm) REVERT: B 746 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7648 (p) REVERT: B 878 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 916 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7897 (mtpp) REVERT: B 967 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7430 (mp) REVERT: B 1002 LYS cc_start: 0.7741 (ptpt) cc_final: 0.7241 (mmtt) REVERT: B 1013 MET cc_start: 0.8916 (mtp) cc_final: 0.8236 (mtp) REVERT: B 1036 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8415 (mm) REVERT: B 1077 ASP cc_start: 0.8106 (p0) cc_final: 0.7809 (p0) REVERT: B 1089 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8236 (tt0) REVERT: B 1134 ARG cc_start: 0.6860 (mpt-90) cc_final: 0.6595 (mpt-90) REVERT: C 60 ASP cc_start: 0.7862 (t70) cc_final: 0.7290 (t0) REVERT: C 63 ILE cc_start: 0.8565 (mm) cc_final: 0.8142 (mt) REVERT: C 74 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8027 (tp30) REVERT: C 82 TYR cc_start: 0.8680 (m-80) cc_final: 0.8164 (m-80) REVERT: C 88 ASN cc_start: 0.8186 (m-40) cc_final: 0.7967 (m110) REVERT: C 89 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.8991 (p) REVERT: C 237 GLN cc_start: 0.7959 (mt0) cc_final: 0.7486 (mm-40) REVERT: D 38 GLN cc_start: 0.6341 (tp40) cc_final: 0.4655 (mt0) REVERT: E 21 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7702 (mt-10) REVERT: E 54 GLN cc_start: 0.8233 (tp-100) cc_final: 0.7315 (mp10) REVERT: E 58 MET cc_start: 0.8281 (mtp) cc_final: 0.7959 (mtp) REVERT: E 164 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7946 (tp) REVERT: F 60 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8333 (mt0) REVERT: F 62 GLU cc_start: 0.7446 (tt0) cc_final: 0.7127 (tt0) REVERT: F 79 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6884 (ptt90) REVERT: F 144 GLU cc_start: 0.8486 (pp20) cc_final: 0.8250 (pp20) REVERT: F 150 GLU cc_start: 0.8882 (pt0) cc_final: 0.8535 (pt0) REVERT: G 71 MET cc_start: 0.8070 (mmm) cc_final: 0.7638 (tpt) REVERT: G 125 TRP cc_start: 0.7326 (t60) cc_final: 0.6930 (t60) REVERT: H 87 ARG cc_start: 0.6957 (tmt170) cc_final: 0.6595 (mmt-90) REVERT: H 89 LEU cc_start: 0.8615 (mt) cc_final: 0.7929 (tt) REVERT: H 126 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6894 (mt-10) REVERT: I 54 ASP cc_start: 0.6678 (t0) cc_final: 0.6366 (t0) REVERT: K 44 ARG cc_start: 0.6543 (mmp-170) cc_final: 0.5360 (mpp-170) REVERT: K 81 MET cc_start: 0.9233 (mmm) cc_final: 0.9027 (mmt) REVERT: K 125 MET cc_start: 0.7448 (mmt) cc_final: 0.6801 (mmp) REVERT: L 30 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8473 (mp) REVERT: N 33 LYS cc_start: 0.5998 (pmmt) cc_final: 0.5409 (mmtt) outliers start: 180 outliers final: 124 residues processed: 658 average time/residue: 0.4480 time to fit residues: 483.9035 Evaluate side-chains 669 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 522 time to evaluate : 4.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1571 SER Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 916 LYS Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 34 LYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain M residue 51 PHE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 107 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 371 optimal weight: 2.9990 chunk 391 optimal weight: 0.7980 chunk 357 optimal weight: 0.9980 chunk 380 optimal weight: 6.9990 chunk 229 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 344 optimal weight: 4.9990 chunk 360 optimal weight: 9.9990 chunk 379 optimal weight: 3.9990 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 592 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 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN ** C 301 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** L 53 HIS ** M 71 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: 0.6980 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35538 Z= 0.204 Angle : 0.637 11.382 48194 Z= 0.319 Chirality : 0.044 0.289 5380 Planarity : 0.004 0.059 6085 Dihedral : 10.645 81.733 5111 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.13 % Favored : 93.85 % Rotamer: Outliers : 4.17 % Allowed : 21.22 % Favored : 74.61 % 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: -1.75 (0.13), residues: 4211 helix: -0.23 (0.15), residues: 1232 sheet: -1.25 (0.21), residues: 567 loop : -1.67 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 525 HIS 0.013 0.001 HIS J 53 PHE 0.019 0.001 PHE A 355 TYR 0.020 0.002 TYR K 78 ARG 0.008 0.000 ARG B1037 *********************** 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 701 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 543 time to evaluate : 4.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8142 (pttp) cc_final: 0.7553 (pttm) REVERT: A 116 HIS cc_start: 0.5095 (t70) cc_final: 0.4838 (t-170) REVERT: A 347 ARG cc_start: 0.7615 (mtt180) cc_final: 0.6686 (tmt170) REVERT: A 446 ARG cc_start: 0.3725 (OUTLIER) cc_final: 0.3345 (mmm160) REVERT: A 472 MET cc_start: 0.8674 (mmp) cc_final: 0.8442 (mmp) REVERT: A 835 LEU cc_start: 0.8178 (pp) cc_final: 0.7783 (pp) REVERT: A 928 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8177 (tmm) REVERT: A 1020 GLN cc_start: 0.7959 (mt0) cc_final: 0.7295 (tt0) REVERT: A 1064 THR cc_start: 0.6652 (OUTLIER) cc_final: 0.6377 (m) REVERT: A 1085 LEU cc_start: 0.8461 (mt) cc_final: 0.7882 (tt) REVERT: A 1175 MET cc_start: 0.8342 (tmm) cc_final: 0.8070 (tmm) REVERT: A 1227 MET cc_start: 0.7768 (mmm) cc_final: 0.6922 (mmm) REVERT: A 1573 TYR cc_start: 0.5056 (OUTLIER) cc_final: 0.4444 (t80) REVERT: A 1588 MET cc_start: 0.9103 (mmm) cc_final: 0.8385 (tpt) REVERT: A 1603 MET cc_start: 0.7909 (ttt) cc_final: 0.7451 (ttp) REVERT: A 1632 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7227 (mm-30) REVERT: A 1634 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7799 (pp) REVERT: B 37 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8750 (mm) REVERT: B 71 LYS cc_start: 0.7520 (mtpp) cc_final: 0.6689 (mmtt) REVERT: B 128 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7188 (mp10) REVERT: B 164 MET cc_start: 0.7890 (ttm) cc_final: 0.7439 (ttp) REVERT: B 205 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7564 (mtt) REVERT: B 286 ARG cc_start: 0.6713 (tpm170) cc_final: 0.5944 (tpm170) REVERT: B 305 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.5747 (tpp-160) REVERT: B 308 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7214 (mm) REVERT: B 373 MET cc_start: 0.8015 (tpp) cc_final: 0.7641 (tpp) REVERT: B 389 CYS cc_start: 0.8281 (m) cc_final: 0.8065 (m) REVERT: B 411 MET cc_start: 0.7988 (mmm) cc_final: 0.7655 (mmm) REVERT: B 434 ARG cc_start: 0.8324 (mmt90) cc_final: 0.7478 (tpt90) REVERT: B 467 THR cc_start: 0.7231 (m) cc_final: 0.6887 (p) REVERT: B 502 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8166 (tmm) REVERT: B 525 TRP cc_start: 0.8032 (t-100) cc_final: 0.7540 (t-100) REVERT: B 606 ASP cc_start: 0.7977 (t0) cc_final: 0.7760 (t0) REVERT: B 667 PHE cc_start: 0.8294 (t80) cc_final: 0.7286 (t80) REVERT: B 668 GLU cc_start: 0.7863 (mm-30) cc_final: 0.6583 (tp30) REVERT: B 746 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7553 (p) REVERT: B 909 ARG cc_start: 0.7509 (mtp85) cc_final: 0.6940 (mtp85) REVERT: B 967 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7424 (mp) REVERT: B 1002 LYS cc_start: 0.7729 (ptpt) cc_final: 0.7244 (mmtt) REVERT: B 1013 MET cc_start: 0.8884 (mtp) cc_final: 0.8190 (mtp) REVERT: B 1037 ARG cc_start: 0.8332 (ttp80) cc_final: 0.8075 (ttp-170) REVERT: B 1089 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8176 (tt0) REVERT: B 1134 ARG cc_start: 0.6742 (mpt-90) cc_final: 0.6523 (mpt-90) REVERT: C 63 ILE cc_start: 0.8566 (mm) cc_final: 0.8170 (mt) REVERT: C 74 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: C 82 TYR cc_start: 0.8782 (m-80) cc_final: 0.8291 (m-80) REVERT: C 88 ASN cc_start: 0.8126 (m-40) cc_final: 0.7899 (m110) REVERT: C 89 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.9005 (p) REVERT: C 237 GLN cc_start: 0.7956 (mt0) cc_final: 0.7486 (mm-40) REVERT: D 38 GLN cc_start: 0.6372 (tp40) cc_final: 0.4762 (mt0) REVERT: D 88 GLN cc_start: 0.7629 (tp40) cc_final: 0.6698 (tm-30) REVERT: E 21 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7682 (mt-10) REVERT: E 54 GLN cc_start: 0.8187 (tp-100) cc_final: 0.7315 (mp10) REVERT: E 164 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7907 (tp) REVERT: F 60 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8343 (mt0) REVERT: F 62 GLU cc_start: 0.7393 (tt0) cc_final: 0.7068 (tt0) REVERT: F 79 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6860 (ptt90) REVERT: F 88 TYR cc_start: 0.8732 (m-80) cc_final: 0.8501 (m-80) REVERT: F 144 GLU cc_start: 0.8443 (pp20) cc_final: 0.8218 (pp20) REVERT: F 150 GLU cc_start: 0.8868 (pt0) cc_final: 0.8527 (pt0) REVERT: G 71 MET cc_start: 0.8029 (mmm) cc_final: 0.7596 (tpt) REVERT: G 125 TRP cc_start: 0.7354 (t60) cc_final: 0.6924 (t60) REVERT: H 87 ARG cc_start: 0.6977 (tmt170) cc_final: 0.6632 (mmt-90) REVERT: H 89 LEU cc_start: 0.8577 (mt) cc_final: 0.7897 (tt) REVERT: H 126 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7093 (mt-10) REVERT: I 54 ASP cc_start: 0.6676 (t0) cc_final: 0.6372 (t0) REVERT: K 44 ARG cc_start: 0.6430 (mmp-170) cc_final: 0.5272 (mpp-170) REVERT: K 52 GLN cc_start: 0.8824 (mp10) cc_final: 0.8115 (mt0) REVERT: K 81 MET cc_start: 0.9235 (mmm) cc_final: 0.9002 (mmt) REVERT: K 140 LYS cc_start: 0.7958 (tppt) cc_final: 0.7716 (ttpp) REVERT: L 29 TYR cc_start: 0.7297 (m-80) cc_final: 0.7039 (m-10) REVERT: L 30 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8483 (mp) REVERT: N 33 LYS cc_start: 0.6005 (pmmt) cc_final: 0.5406 (mmtt) outliers start: 158 outliers final: 118 residues processed: 653 average time/residue: 0.4601 time to fit residues: 496.6976 Evaluate side-chains 664 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 527 time to evaluate : 3.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1571 SER Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 34 LYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 51 PHE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 250 optimal weight: 2.9990 chunk 402 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 422 optimal weight: 10.0000 chunk 388 optimal weight: 0.0470 chunk 336 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 259 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN B 896 GLN ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 HIS ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 35538 Z= 0.318 Angle : 0.701 11.793 48194 Z= 0.355 Chirality : 0.046 0.287 5380 Planarity : 0.005 0.059 6085 Dihedral : 10.778 81.534 5111 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.84 % Favored : 92.14 % Rotamer: Outliers : 4.23 % Allowed : 21.14 % Favored : 74.64 % 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: -0.29 (0.15), residues: 1233 sheet: -1.42 (0.21), residues: 558 loop : -1.73 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 595 HIS 0.014 0.001 HIS J 53 PHE 0.021 0.002 PHE A 355 TYR 0.024 0.002 TYR B 760 ARG 0.007 0.001 ARG B1037 ********************** 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 700 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 540 time to evaluate : 4.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8329 (pttp) cc_final: 0.7669 (pttm) REVERT: A 347 ARG cc_start: 0.7622 (mtt180) cc_final: 0.6823 (tmt170) REVERT: A 433 ASP cc_start: 0.7383 (t0) cc_final: 0.7131 (t0) REVERT: A 446 ARG cc_start: 0.3915 (OUTLIER) cc_final: 0.3387 (mmm160) REVERT: A 830 MET cc_start: 0.8711 (tpt) cc_final: 0.8465 (tpt) REVERT: A 833 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8777 (pp) REVERT: A 835 LEU cc_start: 0.8262 (pp) cc_final: 0.7953 (pp) REVERT: A 1020 GLN cc_start: 0.8048 (mt0) cc_final: 0.7230 (tt0) REVERT: A 1085 LEU cc_start: 0.8477 (mt) cc_final: 0.7844 (tt) REVERT: A 1120 TYR cc_start: 0.7011 (m-80) cc_final: 0.6696 (m-80) REVERT: A 1175 MET cc_start: 0.8344 (tmm) cc_final: 0.8014 (tmm) REVERT: A 1227 MET cc_start: 0.7811 (mmm) cc_final: 0.6877 (mmm) REVERT: A 1464 ASP cc_start: 0.7150 (p0) cc_final: 0.6435 (m-30) REVERT: A 1573 TYR cc_start: 0.5433 (OUTLIER) cc_final: 0.4809 (t80) REVERT: A 1588 MET cc_start: 0.9139 (mmm) cc_final: 0.8394 (tpt) REVERT: A 1603 MET cc_start: 0.8008 (ttt) cc_final: 0.7445 (ttp) REVERT: A 1632 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7238 (mm-30) REVERT: A 1634 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7779 (pp) REVERT: B 37 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8730 (mm) REVERT: B 71 LYS cc_start: 0.7575 (mtpp) cc_final: 0.6822 (mmtt) REVERT: B 128 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: B 205 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7724 (mtt) REVERT: B 305 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.5704 (tpp-160) REVERT: B 308 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7198 (mm) REVERT: B 373 MET cc_start: 0.7985 (tpp) cc_final: 0.7665 (tpp) REVERT: B 377 MET cc_start: 0.6708 (ttm) cc_final: 0.6489 (ttm) REVERT: B 434 ARG cc_start: 0.8468 (mmt90) cc_final: 0.7566 (tpt90) REVERT: B 467 THR cc_start: 0.7316 (m) cc_final: 0.7084 (p) REVERT: B 502 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8448 (tmm) REVERT: B 525 TRP cc_start: 0.8066 (t-100) cc_final: 0.7596 (t-100) REVERT: B 606 ASP cc_start: 0.8019 (t0) cc_final: 0.7788 (t0) REVERT: B 746 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7730 (p) REVERT: B 760 TYR cc_start: 0.8519 (m-80) cc_final: 0.7877 (m-80) REVERT: B 875 HIS cc_start: 0.7751 (p-80) cc_final: 0.7420 (p90) REVERT: B 878 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8141 (tm-30) REVERT: B 909 ARG cc_start: 0.7720 (mtp85) cc_final: 0.7275 (mtp85) REVERT: B 967 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7674 (mp) REVERT: B 975 HIS cc_start: 0.7947 (m170) cc_final: 0.7734 (m170) REVERT: B 1002 LYS cc_start: 0.7789 (ptpt) cc_final: 0.7265 (mmtt) REVERT: B 1013 MET cc_start: 0.8845 (mtp) cc_final: 0.8171 (mtp) REVERT: B 1037 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8209 (ttp-170) REVERT: B 1089 GLN cc_start: 0.8657 (tm-30) cc_final: 0.7845 (tm-30) REVERT: B 1134 ARG cc_start: 0.6744 (mpt-90) cc_final: 0.6543 (mpt-90) REVERT: C 60 ASP cc_start: 0.7879 (t70) cc_final: 0.7330 (t0) REVERT: C 63 ILE cc_start: 0.8534 (mm) cc_final: 0.8127 (mt) REVERT: C 74 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8061 (tp30) REVERT: C 82 TYR cc_start: 0.8833 (m-80) cc_final: 0.8328 (m-80) REVERT: C 89 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8947 (p) REVERT: C 237 GLN cc_start: 0.7985 (mt0) cc_final: 0.7508 (mm-40) REVERT: D 88 GLN cc_start: 0.7705 (tp40) cc_final: 0.6777 (tm-30) REVERT: E 21 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7859 (mt-10) REVERT: E 54 GLN cc_start: 0.8260 (tp-100) cc_final: 0.7319 (mp10) REVERT: E 58 MET cc_start: 0.8446 (mtp) cc_final: 0.7996 (mtp) REVERT: E 133 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7373 (tt0) REVERT: E 164 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7967 (tp) REVERT: F 60 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8346 (mt0) REVERT: F 62 GLU cc_start: 0.7486 (tt0) cc_final: 0.7161 (tt0) REVERT: F 79 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7282 (ptt90) REVERT: F 150 GLU cc_start: 0.8903 (pt0) cc_final: 0.8554 (pt0) REVERT: G 71 MET cc_start: 0.8065 (mmm) cc_final: 0.7668 (tpt) REVERT: G 125 TRP cc_start: 0.7457 (t60) cc_final: 0.7041 (t60) REVERT: H 87 ARG cc_start: 0.6959 (tmt170) cc_final: 0.6590 (mmt180) REVERT: H 89 LEU cc_start: 0.8675 (mt) cc_final: 0.8009 (tt) REVERT: H 126 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6832 (mt-10) REVERT: I 54 ASP cc_start: 0.6699 (t0) cc_final: 0.6416 (t0) REVERT: K 44 ARG cc_start: 0.6470 (mmp-170) cc_final: 0.5258 (mpp-170) REVERT: K 52 GLN cc_start: 0.8808 (mp10) cc_final: 0.8100 (mt0) REVERT: K 140 LYS cc_start: 0.8043 (tppt) cc_final: 0.7747 (ttpp) REVERT: L 29 TYR cc_start: 0.7510 (m-80) cc_final: 0.7304 (m-10) REVERT: L 30 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8556 (mp) REVERT: L 33 GLU cc_start: 0.8245 (pm20) cc_final: 0.8043 (pm20) REVERT: N 33 LYS cc_start: 0.6016 (pmmt) cc_final: 0.5436 (mmtt) outliers start: 160 outliers final: 124 residues processed: 650 average time/residue: 0.4725 time to fit residues: 506.8689 Evaluate side-chains 660 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 518 time to evaluate : 3.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 831 ASP Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1571 SER Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 34 LYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 51 PHE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 267 optimal weight: 0.0980 chunk 358 optimal weight: 8.9990 chunk 103 optimal weight: 0.3980 chunk 310 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 93 optimal weight: 0.0030 chunk 336 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 345 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN ** A 592 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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B 755 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.177014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145813 restraints weight = 52965.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145129 restraints weight = 39339.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.146395 restraints weight = 32680.045| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4947 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= 0.170 Angle : 0.640 11.061 48194 Z= 0.320 Chirality : 0.043 0.272 5380 Planarity : 0.004 0.055 6085 Dihedral : 10.607 83.149 5111 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 3.12 % Allowed : 22.56 % Favored : 74.32 % 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: -1.57 (0.13), residues: 4211 helix: -0.01 (0.15), residues: 1220 sheet: -1.12 (0.21), residues: 563 loop : -1.60 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 525 HIS 0.013 0.001 HIS J 53 PHE 0.021 0.001 PHE A 223 TYR 0.020 0.001 TYR K 78 ARG 0.006 0.000 ARG A 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9011.06 seconds wall clock time: 163 minutes 45.40 seconds (9825.40 seconds total)