Starting phenix.real_space_refine on Mon Sep 14 23:16:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5m5y_3448/09_2026/5m5y_3448_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5m5y_3448/09_2026/5m5y_3448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5m5y_3448/09_2026/5m5y_3448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5m5y_3448/09_2026/5m5y_3448.map" model { file = "/net/cci-nas-00/data/ceres_data/5m5y_3448/09_2026/5m5y_3448_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5m5y_3448/09_2026/5m5y_3448_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 51 5.49 5 S 167 5.16 5 C 21411 2.51 5 N 5915 2.21 5 O 6554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34104 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1466, 11571 Classifications: {'peptide': 1466} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1406} Chain breaks: 7 Chain: "B" Number of atoms: 9301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9301 Classifications: {'peptide': 1170} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1110} Chain breaks: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1751 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1600 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 2 Chain: "H" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1075 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 472 Classifications: {'peptide': 64} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 60} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'TRANS': 42} Chain: "M" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 802 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain breaks: 1 Chain: "N" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1070 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 125} Chain breaks: 3 Chain: "R" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 145 Classifications: {'RNA': 7} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 5} Link IDs: {'rna3p': 6} Chain: "S" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 397 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 781 SG CYS A 102 66.872 103.309 31.265 1.00 78.22 S ATOM 806 SG CYS A 105 69.698 102.102 29.156 1.00 79.63 S ATOM 1609 SG CYS A 233 70.874 105.116 31.082 1.00 71.15 S ATOM 1631 SG CYS A 236 68.654 105.063 28.237 1.00 77.30 S ATOM 461 SG CYS A 62 59.854 56.223 50.582 1.00 65.47 S ATOM 480 SG CYS A 65 62.878 54.299 50.855 1.00 59.54 S ATOM 535 SG CYS A 72 63.324 56.438 52.794 1.00 55.93 S ATOM 20152 SG CYS B1104 76.215 62.298 42.411 1.00 59.16 S ATOM 20178 SG CYS B1107 74.693 64.584 43.018 1.00 61.97 S ATOM 20325 SG CYS B1128 72.672 62.128 42.231 1.00 60.87 S ATOM 20353 SG CYS B1131 74.165 64.660 39.135 1.00 67.87 S ATOM 29069 SG CYS I 10 38.282 139.315 82.408 1.00 99.22 S ATOM 29091 SG CYS I 13 36.062 136.736 81.645 1.00112.15 S ATOM 29211 SG CYS I 30 38.224 136.656 79.042 1.00104.93 S ATOM 29532 SG CYS J 7 75.365 58.025 122.622 1.00 47.69 S ATOM 29555 SG CYS J 10 77.235 55.967 124.489 1.00 45.06 S ATOM 29835 SG CYS J 45 79.061 59.172 124.869 1.00 45.48 S ATOM 29841 SG CYS J 46 76.884 57.407 126.671 1.00 43.47 S ATOM 30866 SG CYS L 31 35.197 55.947 104.675 1.00 66.13 S ATOM 30886 SG CYS L 34 33.375 55.377 107.092 1.00 68.83 S ATOM 30990 SG CYS L 48 31.844 54.573 104.406 1.00 98.70 S ATOM 31013 SG CYS L 51 31.243 57.830 105.750 1.00 76.84 S Time building chain proxies: 7.30, per 1000 atoms: 0.21 Number of scatterers: 34104 At special positions: 0 Unit cell: (156.6, 167.4, 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 6 29.99 S 167 16.00 P 51 15.00 O 6554 8.00 N 5915 7.00 C 21411 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.4 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 B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 27 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7822 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 44 sheets defined 35.0% alpha, 14.9% beta 14 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 22 through 28 removed outlier: 4.313A pdb=" N ASN A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.837A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 175 through 199 removed outlier: 3.721A pdb=" N MET A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 225 removed outlier: 4.113A pdb=" N ASN A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.533A pdb=" N ASN A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.793A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.839A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.675A pdb=" N SER A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 381 through 398 removed outlier: 4.310A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 removed outlier: 3.991A pdb=" N ASP A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 435 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 498 through 505 removed outlier: 3.884A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.718A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 560 removed outlier: 3.788A pdb=" N GLN A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 572 removed outlier: 4.099A pdb=" N THR A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.848A pdb=" N MET A 600 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 removed outlier: 3.980A pdb=" N GLY A 622 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 671 through 681 removed outlier: 3.645A pdb=" N SER A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 removed outlier: 3.784A pdb=" N GLN A 693 " --> pdb=" O ARG A 689 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 792 through 801 removed outlier: 4.082A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 824 removed outlier: 3.914A pdb=" N PHE A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 836 through 847 removed outlier: 3.883A pdb=" N LYS A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TRP A 842 " --> pdb=" O GLU A 838 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.693A pdb=" N ALA A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 883 removed outlier: 4.135A pdb=" N ARG A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 892 through 911 removed outlier: 3.688A pdb=" N VAL A 907 " --> pdb=" O ILE A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 Processing helix chain 'A' and resid 936 through 945 removed outlier: 3.699A pdb=" N GLN A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 943 " --> pdb=" O ASN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1027 removed outlier: 3.829A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A1020 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 4.162A 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 1065 through 1072 removed outlier: 3.955A pdb=" N CYS A1069 " --> pdb=" O GLN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1081 removed outlier: 4.055A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1086 removed outlier: 4.135A pdb=" N ILE A1086 " --> pdb=" O SER A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1109 removed outlier: 3.547A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS A1108 " --> pdb=" O TYR A1104 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A1109 " --> pdb=" O ARG A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1116 removed outlier: 3.803A pdb=" N LYS A1115 " --> pdb=" O PRO A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'A' and resid 1138 through 1150 Processing helix chain 'A' and resid 1163 through 1176 removed outlier: 3.651A pdb=" N ALA A1168 " --> pdb=" O LYS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1193 removed outlier: 3.745A pdb=" N VAL A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1201 removed outlier: 3.695A pdb=" N THR A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1247 through 1259 removed outlier: 3.803A pdb=" N ASP A1252 " --> pdb=" O ASP A1248 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N THR A1253 " --> pdb=" O GLU A1249 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1267 removed outlier: 3.605A pdb=" N VAL A1266 " --> pdb=" O LEU A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1305 Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.524A pdb=" N ILE A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1337 removed outlier: 3.643A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A1337 " --> pdb=" O ILE A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1453 removed outlier: 3.638A pdb=" N ILE A1450 " --> pdb=" O ARG A1446 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS A1453 " --> pdb=" O ALA A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'A' and resid 1485 through 1496 removed outlier: 3.570A pdb=" N VAL A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A1492 " --> pdb=" O ILE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1547 through 1553 Processing helix chain 'A' and resid 1554 through 1572 removed outlier: 3.811A pdb=" N THR A1561 " --> pdb=" O ALA A1557 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A1564 " --> pdb=" O ASN A1560 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.857A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 4.331A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1629 removed outlier: 3.681A pdb=" N ASP A1628 " --> pdb=" O LYS A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1653 removed outlier: 3.566A pdb=" N SER A1653 " --> pdb=" O GLY A1650 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 35 through 41 removed outlier: 4.088A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 52 removed outlier: 3.805A pdb=" N LEU B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 58 through 67 removed outlier: 4.343A pdb=" N ASN B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.624A pdb=" N GLN B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.567A pdb=" N ASN B 224 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 278 removed outlier: 3.730A pdb=" N ILE B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 292 removed outlier: 3.780A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 Processing helix chain 'B' and resid 324 through 334 Processing helix chain 'B' and resid 345 through 357 removed outlier: 4.237A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.818A pdb=" N LEU B 362 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 368 removed outlier: 4.220A pdb=" N GLN B 368 " --> pdb=" O ASP B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 369 through 386 Processing helix chain 'B' and resid 405 through 417 Processing helix chain 'B' and resid 418 through 429 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.629A pdb=" N ARG B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 453 removed outlier: 3.642A pdb=" N ARG B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 493 through 500 Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.804A pdb=" N ALA B 510 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 506 through 512' Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 598 through 614 removed outlier: 3.550A pdb=" N LYS B 602 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 669 removed outlier: 3.632A pdb=" N GLN B 669 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 723 removed outlier: 3.510A pdb=" N GLN B 718 " --> pdb=" O ARG B 714 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N MET B 721 " --> pdb=" O TYR B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 removed outlier: 3.632A pdb=" N ARG B 736 " --> pdb=" O LEU B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.104A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 790 through 796 Processing helix chain 'B' and resid 932 through 936 Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 960 through 976 removed outlier: 3.514A pdb=" N SER B 966 " --> pdb=" O MET B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 removed outlier: 3.973A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1082 removed outlier: 3.747A pdb=" N ASP B1077 " --> pdb=" O GLU B1073 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA B1078 " --> pdb=" O MET B1074 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS B1082 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1093 removed outlier: 4.194A pdb=" N LEU B1088 " --> pdb=" O THR B1084 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B1089 " --> pdb=" O SER B1085 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B1092 " --> pdb=" O LEU B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1192 removed outlier: 3.520A pdb=" N ASP B1186 " --> pdb=" O LEU B1182 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B1188 " --> pdb=" O TYR B1184 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.627A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.668A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.737A pdb=" N LEU C 103 " --> pdb=" O HIS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.801A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 314 through 330 removed outlier: 4.491A pdb=" N ILE C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 48 removed outlier: 4.215A pdb=" N LEU D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 removed outlier: 4.023A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP D 95 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.513A pdb=" N GLU E 21 " --> pdb=" O ARG E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.793A pdb=" N ALA E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 123 removed outlier: 3.942A pdb=" N LYS E 122 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 123 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.752A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 56 through 72 Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.779A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) 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 15 through 20 removed outlier: 3.518A pdb=" N LYS G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 15 through 20' Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 66 through 70 removed outlier: 3.533A pdb=" N VAL G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 removed outlier: 3.859A pdb=" N LEU H 132 " --> pdb=" O TYR H 129 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN H 133 " --> pdb=" O ARG H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 129 through 133' Processing helix chain 'I' and resid 59 through 64 Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.604A pdb=" N ALA J 35 " --> pdb=" O ASP J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 51 removed outlier: 4.069A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.708A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 140 removed outlier: 3.534A pdb=" N ALA K 116 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE K 135 " --> pdb=" O VAL K 131 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 6.538A pdb=" N ILE A 11 " --> pdb=" O GLU B1201 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLU B1201 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER A 13 " --> pdb=" O ASN B1199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA3, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.731A pdb=" N GLU A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 495 removed outlier: 3.632A pdb=" N ALA A 479 " --> pdb=" O ARG B1047 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 543 through 545 removed outlier: 4.303A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 750 through 752 removed outlier: 3.787A pdb=" N CYS A 778 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1031 through 1033 removed outlier: 3.940A pdb=" N SER A1037 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1504 through 1507 removed outlier: 4.470A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1457 through 1460 removed outlier: 6.512A pdb=" N LYS A1473 " --> pdb=" O THR A1458 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TYR A1460 " --> pdb=" O GLU A1471 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU A1471 " --> pdb=" O TYR A1460 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A1291 " --> pdb=" O THR A1273 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A1273 " --> pdb=" O VAL A1291 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A1271 " --> pdb=" O HIS A1293 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1592 through 1593 removed outlier: 4.338A pdb=" N GLN E 179 " --> pdb=" O GLY A1593 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 21 through 24 removed outlier: 4.082A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL G 47 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR G 116 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY G 79 " --> pdb=" O ASN G 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 146 through 147 removed outlier: 4.799A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TRP G 117 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE G 89 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N HIS G 119 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU G 87 " --> pdb=" O HIS G 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 71 through 74 removed outlier: 3.529A pdb=" N LYS B 71 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TRP B 143 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU B 150 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 99 through 104 removed outlier: 4.322A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AB7, first strand: chain 'B' and resid 206 through 209 removed outlier: 3.621A pdb=" N LEU B 206 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.158A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 249 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B 259 " --> pdb=" O HIS B 251 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 592 through 597 removed outlier: 4.016A pdb=" N GLY B 594 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 596 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU B 640 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY B 639 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL B 629 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 660 through 664 Processing sheet with id=AC2, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.621A pdb=" N GLU B 884 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.621A pdb=" N GLU B 884 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 769 through 775 removed outlier: 4.200A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 918 " --> pdb=" O GLN B1034 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 769 through 775 removed outlier: 4.200A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 788 through 789 removed outlier: 3.545A pdb=" N ILE B 788 " --> pdb=" O ILE B 948 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 948 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 823 through 824 removed outlier: 7.641A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA B 860 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LYS B 870 " --> pdb=" O ALA B 860 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AC9, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD1, first strand: chain 'B' and resid 1113 through 1114 Processing sheet with id=AD2, first strand: chain 'B' and resid 1133 through 1134 removed outlier: 4.306A pdb=" N PHE B1167 " --> pdb=" O TRP B1159 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TRP B1159 " --> pdb=" O PHE B1167 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.713A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C 43 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 10.323A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 11.302A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 9.605A pdb=" N PHE C 300 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N THR C 224 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N VAL C 302 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N VAL C 222 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 168 through 169 removed outlier: 7.026A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 168 through 169 removed outlier: 6.143A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.634A pdb=" N THR C 141 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN C 158 " --> pdb=" O THR C 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AD8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AD9, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.983A pdb=" N LEU E 78 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 132 through 135 removed outlier: 3.725A pdb=" N THR G 232 " --> pdb=" O THR G 248 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP G 246 " --> pdb=" O ARG G 234 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL G 236 " --> pdb=" O SER G 244 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N SER G 244 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY G 247 " --> pdb=" O SER G 156 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 167 through 170 Processing sheet with id=AE3, first strand: chain 'H' and resid 95 through 97 removed outlier: 3.714A pdb=" N LEU H 142 " --> pdb=" O MET H 97 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS H 24 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP H 41 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AE5, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AE6, first strand: chain 'N' and resid 30 through 31 removed outlier: 4.033A pdb=" N LYS N 30 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY M 64 " --> pdb=" O LEU M 53 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU M 63 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA M 22 " --> pdb=" O LEU N 110 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR N 108 " --> pdb=" O GLY M 24 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 74 through 81 removed outlier: 3.771A pdb=" N VAL M 77 " --> pdb=" O ILE N 56 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 88 through 92 1102 hydrogen bonds defined for protein. 3000 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 8.51 Time building geometry restraints manager: 3.51 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: 10694 1.34 - 1.46: 5028 1.46 - 1.57: 18774 1.57 - 1.69: 102 1.69 - 1.81: 265 Bond restraints: 34863 Sorted by residual: bond pdb=" N ASP K 57 " pdb=" CA ASP K 57 " ideal model delta sigma weight residual 1.458 1.663 -0.206 1.28e-02 6.10e+03 2.58e+02 bond pdb=" N LYS B1064 " pdb=" CA LYS B1064 " ideal model delta sigma weight residual 1.458 1.562 -0.104 1.30e-02 5.92e+03 6.40e+01 bond pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 1.531 1.647 -0.116 1.59e-02 3.96e+03 5.30e+01 bond pdb=" N GLY A 763 " pdb=" CA GLY A 763 " ideal model delta sigma weight residual 1.449 1.553 -0.104 1.45e-02 4.76e+03 5.16e+01 bond pdb=" CA LYS B1064 " pdb=" CB LYS B1064 " ideal model delta sigma weight residual 1.533 1.597 -0.064 1.60e-02 3.91e+03 1.60e+01 ... (remaining 34858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.90: 47288 7.90 - 15.80: 17 15.80 - 23.69: 5 23.69 - 31.59: 0 31.59 - 39.49: 3 Bond angle restraints: 47313 Sorted by residual: angle pdb=" N ASP K 57 " pdb=" CA ASP K 57 " pdb=" C ASP K 57 " ideal model delta sigma weight residual 112.45 72.96 39.49 1.39e+00 5.18e-01 8.07e+02 angle pdb=" N LYS B1064 " pdb=" CA LYS B1064 " pdb=" C LYS B1064 " ideal model delta sigma weight residual 113.55 78.58 34.97 1.26e+00 6.30e-01 7.70e+02 angle pdb=" N GLY A 445 " pdb=" CA GLY A 445 " pdb=" C GLY A 445 " ideal model delta sigma weight residual 113.18 77.20 35.98 2.37e+00 1.78e-01 2.30e+02 angle pdb=" N SER A 764 " pdb=" CA SER A 764 " pdb=" C SER A 764 " ideal model delta sigma weight residual 108.54 90.62 17.92 1.41e+00 5.03e-01 1.62e+02 angle pdb=" C ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 110.11 87.02 23.09 1.89e+00 2.80e-01 1.49e+02 ... (remaining 47308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 19495 17.97 - 35.94: 1229 35.94 - 53.91: 361 53.91 - 71.88: 56 71.88 - 89.85: 13 Dihedral angle restraints: 21154 sinusoidal: 9055 harmonic: 12099 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 -85.02 -37.58 0 2.50e+00 1.60e-01 2.26e+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 -94.16 -28.44 0 2.50e+00 1.60e-01 1.29e+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 97.17 25.63 0 2.50e+00 1.60e-01 1.05e+02 ... (remaining 21151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.289: 5284 0.289 - 0.579: 5 0.579 - 0.868: 1 0.868 - 1.157: 1 1.157 - 1.447: 1 Chirality restraints: 5292 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 3.96 -1.45 2.00e-01 2.50e+01 5.23e+01 chirality pdb=" CA LYS B1064 " pdb=" N LYS B1064 " pdb=" C LYS B1064 " pdb=" CB LYS B1064 " both_signs ideal model delta sigma weight residual False 2.51 3.64 -1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA ASP A 867 " pdb=" N ASP A 867 " pdb=" C ASP A 867 " pdb=" CB ASP A 867 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 5289 not shown) Planarity restraints: 5936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY K 58 " 0.029 2.00e-02 2.50e+03 5.80e-02 3.37e+01 pdb=" C GLY K 58 " -0.100 2.00e-02 2.50e+03 pdb=" O GLY K 58 " 0.036 2.00e-02 2.50e+03 pdb=" N THR K 59 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 445 " 0.028 2.00e-02 2.50e+03 5.72e-02 3.28e+01 pdb=" C GLY A 445 " -0.099 2.00e-02 2.50e+03 pdb=" O GLY A 445 " 0.034 2.00e-02 2.50e+03 pdb=" N ARG A 446 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 448 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.31e+01 pdb=" C SER A 448 " 0.063 2.00e-02 2.50e+03 pdb=" O SER A 448 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY A 449 " -0.021 2.00e-02 2.50e+03 ... (remaining 5933 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 333 2.56 - 3.15: 27605 3.15 - 3.73: 54207 3.73 - 4.32: 73176 4.32 - 4.90: 116632 Nonbonded interactions: 271953 Sorted by model distance: nonbonded pdb=" N ASP K 57 " pdb=" N GLY K 58 " model vdw 1.976 2.560 nonbonded pdb=" N LYS B1064 " pdb=" N ARG B1065 " model vdw 2.036 2.560 nonbonded pdb=" O LYS A 450 " pdb=" CG2 VAL A 451 " model vdw 2.043 3.460 nonbonded pdb=" OH TYR H 98 " pdb=" OD1 ASN H 139 " model vdw 2.045 3.040 nonbonded pdb=" OG SER M 20 " pdb=" OH TYR M 91 " model vdw 2.163 3.040 ... (remaining 271948 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 38.100 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 40.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 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 : 0.005 0.686 34887 Z= 0.232 Angle : 0.879 45.464 47340 Z= 0.439 Chirality : 0.051 1.447 5292 Planarity : 0.004 0.058 5936 Dihedral : 12.887 89.851 13332 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 1.65 % Allowed : 12.14 % Favored : 86.20 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.11), residues: 4093 helix: -3.46 (0.09), residues: 1220 sheet: -2.64 (0.20), residues: 539 loop : -2.88 (0.11), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 129 TYR 0.013 0.001 TYR B 717 PHE 0.013 0.001 PHE A 269 TRP 0.013 0.001 TRP B 836 HIS 0.004 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.19 (34863) covalent geometry : angle 0.70242 / 0.43 (47313) hydrogen bonds : bond 0.21273 / 13.82 ( 1105) hydrogen bonds : angle 10.46290 / 7.14 ( 3058) metal coordination : bond 0.14938 / 13.95 ( 23) metal coordination : angle 22.16360 / 12.69 ( 27) Misc. bond : bond 0.04514 / 2.38 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 1144 time to evaluate : 1.306 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: 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 24 ILE cc_start: 0.7818 (pt) cc_final: 0.7353 (tp) REVERT: A 221 HIS cc_start: 0.7440 (t-90) cc_final: 0.7180 (t-90) REVERT: A 225 LYS cc_start: 0.6698 (pptt) cc_final: 0.6415 (mmtt) REVERT: A 550 SER cc_start: 0.5996 (p) cc_final: 0.4355 (t) REVERT: A 594 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8576 (t) REVERT: A 613 THR cc_start: 0.7146 (m) cc_final: 0.6668 (p) REVERT: A 633 MET cc_start: 0.8148 (ttm) cc_final: 0.7683 (ttp) REVERT: A 772 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7656 (tppt) REVERT: A 937 ASN cc_start: 0.7054 (t0) cc_final: 0.6717 (t0) REVERT: A 960 MET cc_start: 0.6400 (mmt) cc_final: 0.5980 (mmt) REVERT: A 1027 LEU cc_start: 0.8109 (tp) cc_final: 0.7625 (tp) REVERT: A 1036 ASN cc_start: 0.8736 (t0) cc_final: 0.8520 (t0) REVERT: A 1131 LYS cc_start: 0.6344 (pttt) cc_final: 0.5813 (tppt) REVERT: A 1198 THR cc_start: 0.8933 (m) cc_final: 0.8728 (m) REVERT: A 1223 ARG cc_start: 0.7775 (tmm160) cc_final: 0.7437 (tmt170) REVERT: A 1228 THR cc_start: 0.6715 (p) cc_final: 0.6419 (m) REVERT: A 1309 SER cc_start: 0.6091 (p) cc_final: 0.5845 (t) REVERT: A 1524 VAL cc_start: 0.7061 (t) cc_final: 0.6759 (p) REVERT: A 1624 LYS cc_start: 0.8112 (mptt) cc_final: 0.7860 (mtpt) REVERT: B 22 GLU cc_start: 0.7448 (tp30) cc_final: 0.6795 (tp30) REVERT: B 46 ILE cc_start: 0.7793 (mm) cc_final: 0.7283 (pt) REVERT: B 104 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7704 (pp) REVERT: B 164 MET cc_start: 0.7325 (pmm) cc_final: 0.6894 (pmm) REVERT: B 181 VAL cc_start: 0.9075 (t) cc_final: 0.8716 (m) REVERT: B 275 MET cc_start: 0.6313 (mpm) cc_final: 0.6035 (mmp) REVERT: B 359 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5356 (tt) REVERT: B 549 CYS cc_start: 0.7532 (p) cc_final: 0.7290 (p) REVERT: B 606 ASP cc_start: 0.7450 (p0) cc_final: 0.7153 (p0) REVERT: B 841 ASP cc_start: 0.6584 (m-30) cc_final: 0.6217 (p0) REVERT: B 988 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7463 (tm-30) REVERT: B 1033 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6683 (m-10) REVERT: B 1133 MET cc_start: 0.5288 (tmt) cc_final: 0.4493 (mpp) REVERT: B 1186 ASP cc_start: 0.7282 (p0) cc_final: 0.6923 (p0) REVERT: C 74 GLU cc_start: 0.6919 (pm20) cc_final: 0.6481 (pp20) REVERT: C 89 THR cc_start: 0.8738 (p) cc_final: 0.8471 (t) REVERT: C 159 ASN cc_start: 0.8260 (m-40) cc_final: 0.8003 (m-40) REVERT: C 320 ILE cc_start: 0.6844 (tt) cc_final: 0.5983 (tt) REVERT: D 38 GLN cc_start: 0.5719 (tp-100) cc_final: 0.5228 (mp10) REVERT: E 135 PHE cc_start: 0.7673 (m-80) cc_final: 0.7256 (m-10) REVERT: E 179 GLN cc_start: 0.8337 (tp-100) cc_final: 0.8116 (mt0) REVERT: E 182 ASP cc_start: 0.7691 (t70) cc_final: 0.7273 (t70) REVERT: E 190 LEU cc_start: 0.7452 (mt) cc_final: 0.7029 (tt) REVERT: E 211 TYR cc_start: 0.7562 (m-10) cc_final: 0.7334 (m-10) REVERT: F 60 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.5989 (tt0) REVERT: F 101 ILE cc_start: 0.7649 (tp) cc_final: 0.7356 (tp) REVERT: G 8 ASN cc_start: 0.4323 (OUTLIER) cc_final: 0.1353 (p0) REVERT: G 59 GLN cc_start: 0.6990 (tt0) cc_final: 0.6339 (mp10) REVERT: G 93 ASP cc_start: 0.8028 (p0) cc_final: 0.7757 (p0) REVERT: H 114 VAL cc_start: 0.6925 (m) cc_final: 0.6657 (t) REVERT: J 62 ARG cc_start: 0.6973 (mmm-85) cc_final: 0.6726 (tpp-160) REVERT: J 64 ASN cc_start: 0.7740 (t160) cc_final: 0.7528 (t0) REVERT: K 67 GLU cc_start: 0.6975 (pp20) cc_final: 0.6000 (pp20) REVERT: K 68 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7906 (mm-30) REVERT: K 121 LEU cc_start: 0.6543 (tt) cc_final: 0.6276 (tt) REVERT: K 126 ASP cc_start: 0.8328 (m-30) cc_final: 0.8124 (m-30) REVERT: K 128 CYS cc_start: 0.7079 (p) cc_final: 0.6760 (p) REVERT: K 133 SER cc_start: 0.8848 (m) cc_final: 0.8477 (p) REVERT: L 28 LYS cc_start: 0.5864 (pttm) cc_final: 0.5341 (mmmt) REVERT: M 86 LYS cc_start: 0.5236 (mmtm) cc_final: 0.4839 (pttm) outliers start: 61 outliers final: 10 residues processed: 1183 average time/residue: 0.2233 time to fit residues: 419.7974 Evaluate side-chains 640 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 623 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain L residue 43 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 263 ASN A 264 ASN A 322 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN A 470 HIS A 515 ASN ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS A 926 GLN A 998 HIS ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1141 GLN A1244 ASN A1314 GLN A1436 ASN A1437 ASN ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1592 GLN B 62 ASN B 87 ASN B 231 HIS B 243 GLN B 321 GLN B 499 HIS B 547 HIS B 669 GLN ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 ASN B 886 ASN B1010 ASN ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN B1114 GLN C 99 HIS C 130 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN E 54 GLN F 60 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN I 19 ASN J 64 ASN K 95 HIS ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.177874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.152304 restraints weight = 70053.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.155020 restraints weight = 40298.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.156896 restraints weight = 27506.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.158022 restraints weight = 21254.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.158895 restraints weight = 18125.726| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34887 Z= 0.171 Angle : 0.800 33.948 47340 Z= 0.391 Chirality : 0.047 0.268 5292 Planarity : 0.006 0.073 5936 Dihedral : 11.687 87.338 5129 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 4.61 % Allowed : 17.27 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.12), residues: 4093 helix: -2.10 (0.12), residues: 1203 sheet: -1.95 (0.21), residues: 511 loop : -2.49 (0.12), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1338 TYR 0.035 0.002 TYR A 618 PHE 0.029 0.002 PHE A 91 TRP 0.037 0.002 TRP B 984 HIS 0.009 0.001 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (34863) covalent geometry : angle 0.76329 / 0.39 (47313) hydrogen bonds : bond 0.05318 / 3.50 ( 1105) hydrogen bonds : angle 7.15774 / 4.89 ( 3058) metal coordination : bond 0.01601 / 1.01 ( 23) metal coordination : angle 10.09085 / 6.32 ( 27) Misc. bond : bond 0.00633 / 0.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 686 time to evaluate : 1.309 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.7886 (pt) cc_final: 0.7323 (tp) REVERT: A 221 HIS cc_start: 0.7174 (t-90) cc_final: 0.6813 (t-90) REVERT: A 225 LYS cc_start: 0.6654 (pptt) cc_final: 0.6337 (mmtt) REVERT: A 239 PHE cc_start: 0.7620 (m-80) cc_final: 0.7273 (m-80) REVERT: A 260 GLN cc_start: 0.7780 (mt0) cc_final: 0.7247 (mt0) REVERT: A 528 ASP cc_start: 0.8470 (p0) cc_final: 0.8201 (p0) REVERT: A 589 MET cc_start: 0.8039 (tpp) cc_final: 0.7466 (tpp) REVERT: A 594 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8608 (t) REVERT: A 772 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7751 (tppt) REVERT: A 786 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.6561 (t80) REVERT: A 830 MET cc_start: 0.7972 (tpt) cc_final: 0.7769 (tpt) REVERT: A 946 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7627 (tm) REVERT: A 960 MET cc_start: 0.5939 (mmt) cc_final: 0.5664 (mmt) REVERT: A 1000 MET cc_start: 0.7893 (mtm) cc_final: 0.7530 (mtm) REVERT: A 1049 MET cc_start: 0.6870 (mtp) cc_final: 0.6427 (mtm) REVERT: A 1146 SER cc_start: 0.9060 (m) cc_final: 0.8148 (t) REVERT: A 1223 ARG cc_start: 0.7863 (tmm160) cc_final: 0.7405 (tmt170) REVERT: A 1227 MET cc_start: 0.7749 (mpt) cc_final: 0.7501 (mpt) REVERT: A 1335 LYS cc_start: 0.6689 (mmmt) cc_final: 0.6324 (ttmt) REVERT: A 1441 LYS cc_start: 0.7061 (tptt) cc_final: 0.6741 (tttm) REVERT: A 1566 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8059 (mt) REVERT: A 1611 MET cc_start: 0.7447 (mmm) cc_final: 0.7017 (mmm) REVERT: B 46 ILE cc_start: 0.7961 (mm) cc_final: 0.7423 (pt) REVERT: B 181 VAL cc_start: 0.9132 (t) cc_final: 0.8844 (m) REVERT: B 205 MET cc_start: 0.8124 (mmm) cc_final: 0.7722 (mtt) REVERT: B 275 MET cc_start: 0.6262 (mpm) cc_final: 0.5899 (mmp) REVERT: B 450 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8436 (tt) REVERT: B 473 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7379 (tm-30) REVERT: B 481 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8745 (p) REVERT: B 511 GLN cc_start: 0.7680 (pt0) cc_final: 0.6583 (tp40) REVERT: B 513 LYS cc_start: 0.6595 (tptt) cc_final: 0.6395 (tptm) REVERT: B 550 ARG cc_start: 0.7119 (tmt170) cc_final: 0.6684 (tmm-80) REVERT: B 606 ASP cc_start: 0.7614 (p0) cc_final: 0.7320 (p0) REVERT: B 672 MET cc_start: 0.7435 (ppp) cc_final: 0.7128 (ppp) REVERT: B 765 PHE cc_start: 0.7982 (m-80) cc_final: 0.7688 (m-80) REVERT: B 773 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7170 (t) REVERT: B 808 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7897 (ttmm) REVERT: B 840 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6382 (mp) REVERT: B 1033 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.6765 (m-10) REVERT: B 1133 MET cc_start: 0.5081 (tmt) cc_final: 0.4565 (mpp) REVERT: B 1151 ILE cc_start: 0.2302 (OUTLIER) cc_final: 0.1767 (tp) REVERT: B 1192 MET cc_start: 0.7569 (mtt) cc_final: 0.7347 (ttm) REVERT: C 89 THR cc_start: 0.8770 (p) cc_final: 0.8473 (t) REVERT: D 38 GLN cc_start: 0.5654 (tp-100) cc_final: 0.4917 (mp10) REVERT: E 135 PHE cc_start: 0.7466 (m-80) cc_final: 0.7042 (m-10) REVERT: E 144 ILE cc_start: 0.8166 (pp) cc_final: 0.7957 (pp) REVERT: E 179 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8064 (mt0) REVERT: E 182 ASP cc_start: 0.7768 (t70) cc_final: 0.7329 (t70) REVERT: E 190 LEU cc_start: 0.7741 (mt) cc_final: 0.6980 (tt) REVERT: F 64 ILE cc_start: 0.7423 (mm) cc_final: 0.6886 (mp) REVERT: F 86 THR cc_start: 0.7302 (p) cc_final: 0.7054 (p) REVERT: G 8 ASN cc_start: 0.4256 (OUTLIER) cc_final: 0.1908 (p0) REVERT: G 59 GLN cc_start: 0.7340 (tt0) cc_final: 0.6460 (mp10) REVERT: H 49 VAL cc_start: 0.6758 (t) cc_final: 0.6558 (p) REVERT: H 109 LYS cc_start: 0.8683 (tmtt) cc_final: 0.8105 (tmtt) REVERT: I 2 SER cc_start: 0.7964 (m) cc_final: 0.7537 (t) REVERT: J 49 MET cc_start: 0.8118 (mmt) cc_final: 0.7688 (mmm) REVERT: J 64 ASN cc_start: 0.7581 (t0) cc_final: 0.6943 (t0) REVERT: K 67 GLU cc_start: 0.7043 (pp20) cc_final: 0.6124 (pp20) REVERT: K 68 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8268 (mm-30) REVERT: K 122 LYS cc_start: 0.8318 (tppt) cc_final: 0.7835 (ptmm) REVERT: K 125 MET cc_start: 0.7350 (mmm) cc_final: 0.7060 (mmm) REVERT: K 128 CYS cc_start: 0.7039 (p) cc_final: 0.6808 (p) REVERT: K 133 SER cc_start: 0.8335 (m) cc_final: 0.8063 (p) REVERT: L 28 LYS cc_start: 0.5761 (pttm) cc_final: 0.5522 (mmmt) REVERT: L 64 LEU cc_start: 0.7030 (tp) cc_final: 0.6713 (tt) REVERT: M 86 LYS cc_start: 0.5812 (mmtm) cc_final: 0.5174 (pttm) outliers start: 170 outliers final: 65 residues processed: 814 average time/residue: 0.2163 time to fit residues: 289.8578 Evaluate side-chains 632 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 554 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1619 CYS Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 808 LYS Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 1015 SER Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 95 HIS Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 26 optimal weight: 9.9990 chunk 370 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 376 optimal weight: 3.9990 chunk 346 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1088 HIS ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 243 GLN B 547 HIS ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN B 767 ASN ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN G 8 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.168437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141919 restraints weight = 70721.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.144571 restraints weight = 41877.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.146235 restraints weight = 29089.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.147395 restraints weight = 23027.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.148011 restraints weight = 19813.711| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 34887 Z= 0.268 Angle : 0.843 33.258 47340 Z= 0.420 Chirality : 0.050 0.311 5292 Planarity : 0.006 0.079 5936 Dihedral : 11.816 88.119 5117 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.53 % Favored : 91.38 % Rotamer: Outliers : 5.53 % Allowed : 18.92 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.12), residues: 4093 helix: -1.65 (0.13), residues: 1242 sheet: -1.93 (0.22), residues: 527 loop : -2.36 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 920 TYR 0.048 0.003 TYR B 717 PHE 0.026 0.003 PHE C 219 TRP 0.015 0.002 TRP B 611 HIS 0.014 0.002 HIS B 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.27 (34863) covalent geometry : angle 0.81593 / 0.42 (47313) hydrogen bonds : bond 0.05280 / 3.47 ( 1105) hydrogen bonds : angle 6.67610 / 4.57 ( 3058) metal coordination : bond 0.01302 / 0.81 ( 23) metal coordination : angle 8.88647 / 5.43 ( 27) Misc. bond : bond 0.00149 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 570 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.6456 (t0) cc_final: 0.5921 (m-30) REVERT: A 24 ILE cc_start: 0.8060 (pt) cc_final: 0.7663 (tp) REVERT: A 207 SER cc_start: 0.8470 (t) cc_final: 0.8264 (p) REVERT: A 528 ASP cc_start: 0.8565 (p0) cc_final: 0.8336 (p0) REVERT: A 744 MET cc_start: 0.7969 (tpt) cc_final: 0.7624 (mmt) REVERT: A 756 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6258 (tmtt) REVERT: A 772 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7560 (tppt) REVERT: A 833 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7925 (tt) REVERT: A 926 GLN cc_start: 0.8142 (tp40) cc_final: 0.7789 (tp-100) REVERT: A 937 ASN cc_start: 0.7696 (t0) cc_final: 0.7111 (t0) REVERT: A 946 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7971 (tm) REVERT: A 960 MET cc_start: 0.5837 (mmt) cc_final: 0.5095 (mmt) REVERT: A 977 MET cc_start: 0.7587 (ttt) cc_final: 0.7229 (ttt) REVERT: A 997 PHE cc_start: 0.7557 (m-80) cc_final: 0.7292 (m-80) REVERT: A 1000 MET cc_start: 0.7864 (mtm) cc_final: 0.7389 (mtm) REVERT: A 1078 LYS cc_start: 0.7269 (tttt) cc_final: 0.6773 (tttt) REVERT: A 1146 SER cc_start: 0.8987 (m) cc_final: 0.8201 (t) REVERT: A 1223 ARG cc_start: 0.7939 (tmm160) cc_final: 0.7529 (tmt170) REVERT: A 1227 MET cc_start: 0.8062 (mpt) cc_final: 0.7699 (mpt) REVERT: A 1235 THR cc_start: 0.5090 (OUTLIER) cc_final: 0.4831 (t) REVERT: A 1441 LYS cc_start: 0.6749 (tptt) cc_final: 0.6520 (tttm) REVERT: A 1485 MET cc_start: 0.5628 (mmm) cc_final: 0.5378 (mmm) REVERT: A 1499 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.5897 (ptt-90) REVERT: A 1611 MET cc_start: 0.7526 (mmm) cc_final: 0.7070 (tpp) REVERT: B 46 ILE cc_start: 0.8109 (mm) cc_final: 0.7403 (pt) REVERT: B 275 MET cc_start: 0.6669 (mpm) cc_final: 0.6381 (mmp) REVERT: B 446 MET cc_start: 0.7856 (tpt) cc_final: 0.7116 (tpt) REVERT: B 481 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8785 (p) REVERT: B 511 GLN cc_start: 0.7777 (pt0) cc_final: 0.7567 (pm20) REVERT: B 513 LYS cc_start: 0.6695 (tptt) cc_final: 0.6456 (tptm) REVERT: B 566 TYR cc_start: 0.7142 (t80) cc_final: 0.6754 (t80) REVERT: B 643 PHE cc_start: 0.7678 (t80) cc_final: 0.7410 (t80) REVERT: B 679 GLN cc_start: 0.8413 (mp10) cc_final: 0.7815 (mp10) REVERT: B 762 MET cc_start: 0.7949 (mpt) cc_final: 0.7746 (mmt) REVERT: B 773 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.7880 (t) REVERT: B 805 LYS cc_start: 0.7858 (tppt) cc_final: 0.7575 (ttpt) REVERT: B 946 ASP cc_start: 0.7934 (m-30) cc_final: 0.7507 (m-30) REVERT: B 1007 TYR cc_start: 0.8390 (t80) cc_final: 0.8063 (t80) REVERT: B 1033 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: B 1133 MET cc_start: 0.5407 (tmt) cc_final: 0.4680 (mpp) REVERT: B 1151 ILE cc_start: 0.2414 (OUTLIER) cc_final: 0.1637 (tp) REVERT: C 44 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7046 (pt) REVERT: C 134 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7522 (tm) REVERT: D 23 HIS cc_start: 0.5177 (OUTLIER) cc_final: 0.4603 (m170) REVERT: D 38 GLN cc_start: 0.5969 (tp-100) cc_final: 0.4904 (mp10) REVERT: E 135 PHE cc_start: 0.7503 (m-80) cc_final: 0.6945 (m-10) REVERT: E 179 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8335 (tp-100) REVERT: E 182 ASP cc_start: 0.7910 (t70) cc_final: 0.7606 (t70) REVERT: E 190 LEU cc_start: 0.7962 (mt) cc_final: 0.7035 (tt) REVERT: F 65 ARG cc_start: 0.7483 (ttp-170) cc_final: 0.7279 (ttp-170) REVERT: G 59 GLN cc_start: 0.7691 (tt0) cc_final: 0.6685 (mp10) REVERT: G 90 LEU cc_start: 0.8040 (mp) cc_final: 0.7522 (mp) REVERT: G 119 HIS cc_start: 0.6689 (m-70) cc_final: 0.6335 (m-70) REVERT: H 7 ASP cc_start: 0.8003 (t0) cc_final: 0.7365 (p0) REVERT: H 49 VAL cc_start: 0.7123 (t) cc_final: 0.6858 (p) REVERT: H 57 VAL cc_start: 0.8047 (t) cc_final: 0.7838 (t) REVERT: H 97 MET cc_start: 0.7658 (ttm) cc_final: 0.7395 (ttm) REVERT: I 2 SER cc_start: 0.7848 (m) cc_final: 0.7545 (t) REVERT: J 49 MET cc_start: 0.8461 (mmt) cc_final: 0.8205 (mmm) REVERT: J 55 ASP cc_start: 0.7833 (t0) cc_final: 0.7628 (t0) REVERT: J 64 ASN cc_start: 0.8162 (t0) cc_final: 0.7609 (t0) REVERT: K 69 ASP cc_start: 0.8475 (t0) cc_final: 0.8250 (t0) REVERT: K 122 LYS cc_start: 0.8353 (tppt) cc_final: 0.7912 (ttpp) REVERT: K 125 MET cc_start: 0.7437 (mmm) cc_final: 0.7121 (mmm) REVERT: K 128 CYS cc_start: 0.7327 (p) cc_final: 0.6988 (p) REVERT: L 64 LEU cc_start: 0.7325 (tp) cc_final: 0.7110 (tt) REVERT: M 53 LEU cc_start: 0.6402 (tt) cc_final: 0.5233 (mt) REVERT: M 86 LYS cc_start: 0.6091 (mmtm) cc_final: 0.5314 (pttm) outliers start: 204 outliers final: 114 residues processed: 722 average time/residue: 0.2136 time to fit residues: 256.1973 Evaluate side-chains 617 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 490 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1499 ARG Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1619 CYS Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 420 TYR Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1015 SER Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 270 optimal weight: 6.9990 chunk 343 optimal weight: 0.7980 chunk 243 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 309 optimal weight: 9.9990 chunk 80 optimal weight: 0.1980 chunk 304 optimal weight: 6.9990 chunk 282 optimal weight: 8.9990 chunk 7 optimal weight: 30.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1088 HIS ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 168 ASN B 243 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 669 GLN ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.168928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.142709 restraints weight = 69909.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.145343 restraints weight = 41126.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.147059 restraints weight = 28501.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.148173 restraints weight = 22459.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.148735 restraints weight = 19279.344| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 34887 Z= 0.190 Angle : 0.763 28.041 47340 Z= 0.377 Chirality : 0.047 0.240 5292 Planarity : 0.005 0.078 5936 Dihedral : 11.824 89.252 5113 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.23 % Favored : 91.69 % Rotamer: Outliers : 5.39 % Allowed : 19.79 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.12), residues: 4093 helix: -1.34 (0.14), residues: 1266 sheet: -1.86 (0.22), residues: 531 loop : -2.27 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 25 TYR 0.042 0.002 TYR B1032 PHE 0.031 0.002 PHE A1535 TRP 0.031 0.002 TRP B 143 HIS 0.009 0.001 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (34863) covalent geometry : angle 0.73836 / 0.37 (47313) hydrogen bonds : bond 0.04625 / 3.04 ( 1105) hydrogen bonds : angle 6.33221 / 4.33 ( 3058) metal coordination : bond 0.01446 / 0.82 ( 23) metal coordination : angle 8.03746 / 4.81 ( 27) Misc. bond : bond 0.00260 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 571 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.6484 (t0) cc_final: 0.5883 (m-30) REVERT: A 24 ILE cc_start: 0.8099 (pt) cc_final: 0.7845 (tp) REVERT: A 528 ASP cc_start: 0.8508 (p0) cc_final: 0.8284 (p0) REVERT: A 756 LYS cc_start: 0.6672 (OUTLIER) cc_final: 0.6172 (tmtt) REVERT: A 772 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7682 (tppt) REVERT: A 833 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7855 (tt) REVERT: A 925 MET cc_start: 0.8278 (tmm) cc_final: 0.8021 (tmm) REVERT: A 946 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7984 (tm) REVERT: A 977 MET cc_start: 0.7681 (ttt) cc_final: 0.7401 (ttt) REVERT: A 1000 MET cc_start: 0.7811 (mtm) cc_final: 0.7371 (mtm) REVERT: A 1146 SER cc_start: 0.9004 (m) cc_final: 0.8160 (t) REVERT: A 1223 ARG cc_start: 0.7980 (tmm160) cc_final: 0.7465 (tmt170) REVERT: A 1227 MET cc_start: 0.7934 (mpt) cc_final: 0.7567 (mpt) REVERT: A 1441 LYS cc_start: 0.6844 (tptt) cc_final: 0.6535 (tttm) REVERT: A 1569 VAL cc_start: 0.8665 (p) cc_final: 0.8408 (t) REVERT: A 1575 ILE cc_start: 0.8168 (pp) cc_final: 0.7876 (tp) REVERT: A 1611 MET cc_start: 0.7228 (mmm) cc_final: 0.6792 (tpp) REVERT: B 46 ILE cc_start: 0.8035 (mm) cc_final: 0.7315 (pt) REVERT: B 473 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7948 (tm-30) REVERT: B 481 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8758 (p) REVERT: B 511 GLN cc_start: 0.7725 (pt0) cc_final: 0.7432 (pm20) REVERT: B 566 TYR cc_start: 0.7084 (t80) cc_final: 0.6736 (t80) REVERT: B 773 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.7787 (t) REVERT: B 805 LYS cc_start: 0.7922 (tppt) cc_final: 0.7631 (ttpt) REVERT: B 935 ASP cc_start: 0.7320 (t0) cc_final: 0.6996 (t70) REVERT: B 946 ASP cc_start: 0.7970 (m-30) cc_final: 0.7545 (m-30) REVERT: B 1007 TYR cc_start: 0.8388 (t80) cc_final: 0.7874 (t80) REVERT: B 1033 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6807 (m-10) REVERT: B 1133 MET cc_start: 0.5158 (tmt) cc_final: 0.4721 (mpp) REVERT: B 1151 ILE cc_start: 0.2449 (OUTLIER) cc_final: 0.1622 (tp) REVERT: B 1186 ASP cc_start: 0.7616 (p0) cc_final: 0.7255 (p0) REVERT: B 1192 MET cc_start: 0.7798 (mtt) cc_final: 0.7534 (ttm) REVERT: C 134 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7499 (tm) REVERT: D 23 HIS cc_start: 0.5382 (OUTLIER) cc_final: 0.5031 (m170) REVERT: D 38 GLN cc_start: 0.6023 (tp-100) cc_final: 0.4926 (mp10) REVERT: E 135 PHE cc_start: 0.7421 (m-80) cc_final: 0.6895 (m-10) REVERT: E 137 GLU cc_start: 0.7234 (pt0) cc_final: 0.6881 (pt0) REVERT: E 179 GLN cc_start: 0.8533 (tp-100) cc_final: 0.8054 (tp-100) REVERT: E 182 ASP cc_start: 0.7832 (t70) cc_final: 0.7603 (t70) REVERT: E 190 LEU cc_start: 0.7960 (mt) cc_final: 0.6947 (tp) REVERT: G 59 GLN cc_start: 0.7762 (tt0) cc_final: 0.6841 (mp10) REVERT: G 90 LEU cc_start: 0.8004 (mp) cc_final: 0.7452 (mp) REVERT: G 119 HIS cc_start: 0.6617 (m-70) cc_final: 0.6242 (m-70) REVERT: G 123 TYR cc_start: 0.7425 (m-80) cc_final: 0.7165 (m-80) REVERT: H 97 MET cc_start: 0.7975 (ttm) cc_final: 0.7696 (ttm) REVERT: I 2 SER cc_start: 0.7735 (m) cc_final: 0.7446 (t) REVERT: J 49 MET cc_start: 0.8454 (mmt) cc_final: 0.8158 (mmm) REVERT: J 62 ARG cc_start: 0.7306 (ttm-80) cc_final: 0.6942 (tpp-160) REVERT: J 64 ASN cc_start: 0.8230 (t0) cc_final: 0.7578 (t0) REVERT: K 67 GLU cc_start: 0.6825 (pp20) cc_final: 0.6017 (pp20) REVERT: K 68 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8234 (mm-30) REVERT: K 69 ASP cc_start: 0.8489 (t0) cc_final: 0.8105 (t0) REVERT: K 122 LYS cc_start: 0.8245 (tppt) cc_final: 0.7882 (ttpp) REVERT: K 125 MET cc_start: 0.7201 (mmm) cc_final: 0.6724 (tpp) REVERT: K 128 CYS cc_start: 0.7468 (p) cc_final: 0.7147 (p) REVERT: L 33 GLU cc_start: 0.7420 (mp0) cc_final: 0.6788 (pm20) REVERT: L 49 LYS cc_start: 0.5903 (mppt) cc_final: 0.5610 (ttmt) REVERT: L 64 LEU cc_start: 0.7607 (tp) cc_final: 0.7315 (tt) REVERT: M 53 LEU cc_start: 0.6327 (tt) cc_final: 0.5088 (mt) REVERT: M 75 GLN cc_start: 0.4288 (tt0) cc_final: 0.3942 (tt0) REVERT: N 107 MET cc_start: 0.5361 (tpt) cc_final: 0.3582 (mpp) outliers start: 199 outliers final: 115 residues processed: 723 average time/residue: 0.1920 time to fit residues: 235.8298 Evaluate side-chains 628 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 503 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1619 CYS Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 420 TYR Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1015 SER Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 160 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 56 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 chunk 399 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 370 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1088 HIS A1314 GLN A1443 GLN ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1662 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN B 950 ASN ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN G 59 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 ASN ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.166491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140162 restraints weight = 70393.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142697 restraints weight = 41424.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.144416 restraints weight = 28789.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.145510 restraints weight = 22670.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.146132 restraints weight = 19513.224| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 34887 Z= 0.213 Angle : 0.779 29.092 47340 Z= 0.388 Chirality : 0.048 0.260 5292 Planarity : 0.005 0.075 5936 Dihedral : 11.897 88.328 5113 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.36 % Favored : 90.57 % Rotamer: Outliers : 6.21 % Allowed : 20.38 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.12), residues: 4093 helix: -1.12 (0.14), residues: 1246 sheet: -1.85 (0.22), residues: 527 loop : -2.23 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1176 TYR 0.050 0.002 TYR A 514 PHE 0.036 0.002 PHE A1535 TRP 0.026 0.002 TRP B 143 HIS 0.009 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (34863) covalent geometry : angle 0.75712 / 0.39 (47313) hydrogen bonds : bond 0.04556 / 3.02 ( 1105) hydrogen bonds : angle 6.22813 / 4.27 ( 3058) metal coordination : bond 0.01296 / 0.71 ( 23) metal coordination : angle 7.73018 / 4.38 ( 27) Misc. bond : bond 0.00191 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 555 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.6482 (t0) cc_final: 0.5877 (m-30) REVERT: A 24 ILE cc_start: 0.8126 (pt) cc_final: 0.7886 (tp) REVERT: A 390 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8866 (mm) REVERT: A 528 ASP cc_start: 0.8508 (p0) cc_final: 0.8307 (p0) REVERT: A 604 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7419 (tptp) REVERT: A 756 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.6304 (tmtt) REVERT: A 772 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7473 (tppt) REVERT: A 833 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7806 (tt) REVERT: A 925 MET cc_start: 0.8328 (tmm) cc_final: 0.8108 (tmm) REVERT: A 926 GLN cc_start: 0.8248 (tp-100) cc_final: 0.8033 (tp40) REVERT: A 946 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8196 (tm) REVERT: A 977 MET cc_start: 0.7699 (ttt) cc_final: 0.7401 (ttt) REVERT: A 997 PHE cc_start: 0.7353 (m-80) cc_final: 0.7051 (m-80) REVERT: A 1000 MET cc_start: 0.7695 (mtm) cc_final: 0.7215 (mtm) REVERT: A 1146 SER cc_start: 0.8993 (m) cc_final: 0.8142 (t) REVERT: A 1223 ARG cc_start: 0.8099 (tmm160) cc_final: 0.7646 (tmt170) REVERT: A 1227 MET cc_start: 0.8003 (mpt) cc_final: 0.7585 (mpt) REVERT: A 1441 LYS cc_start: 0.6480 (tptt) cc_final: 0.6265 (tttm) REVERT: A 1569 VAL cc_start: 0.8777 (p) cc_final: 0.8517 (t) REVERT: A 1575 ILE cc_start: 0.8288 (pp) cc_final: 0.7951 (tp) REVERT: A 1592 GLN cc_start: 0.7408 (tm-30) cc_final: 0.7009 (tm-30) REVERT: A 1611 MET cc_start: 0.7287 (mmm) cc_final: 0.7058 (tpp) REVERT: B 46 ILE cc_start: 0.8190 (mm) cc_final: 0.7494 (pt) REVERT: B 446 MET cc_start: 0.7630 (tpt) cc_final: 0.7412 (tpt) REVERT: B 473 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7714 (tm-30) REVERT: B 481 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8778 (p) REVERT: B 511 GLN cc_start: 0.7477 (pt0) cc_final: 0.7209 (pm20) REVERT: B 717 TYR cc_start: 0.7333 (t80) cc_final: 0.7099 (t80) REVERT: B 805 LYS cc_start: 0.7982 (tppt) cc_final: 0.7598 (ttpt) REVERT: B 946 ASP cc_start: 0.7963 (m-30) cc_final: 0.7506 (m-30) REVERT: B 1007 TYR cc_start: 0.8472 (t80) cc_final: 0.7857 (t80) REVERT: B 1033 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.7149 (m-10) REVERT: B 1133 MET cc_start: 0.5180 (tmt) cc_final: 0.4722 (mpp) REVERT: C 134 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7735 (tm) REVERT: D 23 HIS cc_start: 0.5347 (OUTLIER) cc_final: 0.4947 (m170) REVERT: D 38 GLN cc_start: 0.6277 (tp-100) cc_final: 0.5111 (mp10) REVERT: E 135 PHE cc_start: 0.7421 (m-80) cc_final: 0.7023 (m-10) REVERT: E 137 GLU cc_start: 0.7248 (pt0) cc_final: 0.7035 (pt0) REVERT: E 163 GLU cc_start: 0.7231 (pt0) cc_final: 0.6821 (tp30) REVERT: E 179 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8422 (tp40) REVERT: G 59 GLN cc_start: 0.7808 (tt0) cc_final: 0.6668 (mp10) REVERT: G 90 LEU cc_start: 0.8028 (mp) cc_final: 0.7329 (mt) REVERT: G 119 HIS cc_start: 0.6297 (m-70) cc_final: 0.6088 (m-70) REVERT: G 123 TYR cc_start: 0.7725 (m-80) cc_final: 0.7449 (m-80) REVERT: H 27 GLU cc_start: 0.6870 (mp0) cc_final: 0.6659 (mp0) REVERT: H 97 MET cc_start: 0.7968 (ttm) cc_final: 0.7754 (ttm) REVERT: I 2 SER cc_start: 0.7846 (m) cc_final: 0.7553 (t) REVERT: J 64 ASN cc_start: 0.8157 (t0) cc_final: 0.7560 (t0) REVERT: K 67 GLU cc_start: 0.6692 (pp20) cc_final: 0.5778 (pp20) REVERT: K 68 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8173 (mm-30) REVERT: K 69 ASP cc_start: 0.8584 (t0) cc_final: 0.8064 (t0) REVERT: K 114 VAL cc_start: 0.7716 (p) cc_final: 0.7471 (t) REVERT: K 122 LYS cc_start: 0.8406 (tppt) cc_final: 0.8182 (ttpp) REVERT: K 125 MET cc_start: 0.7271 (mmm) cc_final: 0.6968 (tpp) REVERT: K 128 CYS cc_start: 0.7571 (p) cc_final: 0.7253 (p) REVERT: L 33 GLU cc_start: 0.7504 (mp0) cc_final: 0.6904 (pm20) REVERT: L 49 LYS cc_start: 0.5704 (mppt) cc_final: 0.5407 (ttmt) REVERT: M 53 LEU cc_start: 0.6495 (tt) cc_final: 0.5286 (mt) REVERT: M 75 GLN cc_start: 0.4851 (tt0) cc_final: 0.4525 (tt0) REVERT: N 107 MET cc_start: 0.5349 (OUTLIER) cc_final: 0.3659 (mpp) outliers start: 229 outliers final: 140 residues processed: 728 average time/residue: 0.1972 time to fit residues: 241.7674 Evaluate side-chains 651 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 501 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1619 CYS Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 420 TYR Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 463 TYR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1015 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 160 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 339 optimal weight: 4.9990 chunk 373 optimal weight: 0.5980 chunk 394 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 276 optimal weight: 8.9990 chunk 368 optimal weight: 3.9990 chunk 316 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1088 HIS ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 646 HIS ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 ASN B 767 ASN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.167297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141251 restraints weight = 69616.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143735 restraints weight = 41405.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.145360 restraints weight = 29052.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.146437 restraints weight = 23113.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.147027 restraints weight = 20042.729| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34887 Z= 0.177 Angle : 0.764 22.700 47340 Z= 0.377 Chirality : 0.048 0.452 5292 Planarity : 0.005 0.065 5936 Dihedral : 11.895 86.831 5113 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.67 % Favored : 91.25 % Rotamer: Outliers : 5.56 % Allowed : 21.88 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.13), residues: 4093 helix: -0.92 (0.14), residues: 1234 sheet: -1.75 (0.22), residues: 555 loop : -2.14 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 169 TYR 0.032 0.002 TYR A 514 PHE 0.043 0.002 PHE A1535 TRP 0.016 0.002 TRP B 143 HIS 0.008 0.001 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (34863) covalent geometry : angle 0.74691 / 0.38 (47313) hydrogen bonds : bond 0.04346 / 2.89 ( 1105) hydrogen bonds : angle 6.08132 / 4.17 ( 3058) metal coordination : bond 0.01383 / 0.80 ( 23) metal coordination : angle 6.78508 / 3.99 ( 27) Misc. bond : bond 0.00246 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 545 time to evaluate : 1.327 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 15 ASP cc_start: 0.6560 (t0) cc_final: 0.5861 (m-30) REVERT: A 24 ILE cc_start: 0.8098 (pt) cc_final: 0.7818 (tp) REVERT: A 226 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.6919 (mmmt) REVERT: A 390 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 604 LYS cc_start: 0.7767 (mmmt) cc_final: 0.7420 (tptp) REVERT: A 756 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.6272 (tmtt) REVERT: A 772 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7699 (tppt) REVERT: A 925 MET cc_start: 0.8272 (tmm) cc_final: 0.8059 (tmm) REVERT: A 946 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8145 (tm) REVERT: A 977 MET cc_start: 0.7708 (ttt) cc_final: 0.7410 (ttt) REVERT: A 997 PHE cc_start: 0.7306 (m-80) cc_final: 0.6864 (m-80) REVERT: A 1000 MET cc_start: 0.7629 (mtm) cc_final: 0.7128 (mtm) REVERT: A 1146 SER cc_start: 0.9036 (m) cc_final: 0.8262 (t) REVERT: A 1223 ARG cc_start: 0.8110 (tmm160) cc_final: 0.7683 (tmt170) REVERT: A 1227 MET cc_start: 0.8001 (mpt) cc_final: 0.7580 (mpt) REVERT: A 1439 MET cc_start: 0.1540 (tmm) cc_final: 0.1229 (tmm) REVERT: A 1485 MET cc_start: 0.5482 (mmm) cc_final: 0.5273 (mmm) REVERT: A 1535 PHE cc_start: 0.7140 (m-10) cc_final: 0.6906 (m-10) REVERT: A 1575 ILE cc_start: 0.8281 (pp) cc_final: 0.7944 (tp) REVERT: A 1592 GLN cc_start: 0.7510 (tm-30) cc_final: 0.7044 (tm-30) REVERT: A 1611 MET cc_start: 0.7294 (mmm) cc_final: 0.6951 (tpp) REVERT: B 46 ILE cc_start: 0.8117 (mm) cc_final: 0.7381 (pt) REVERT: B 306 LEU cc_start: 0.7455 (pp) cc_final: 0.7252 (tp) REVERT: B 446 MET cc_start: 0.7659 (tpt) cc_final: 0.7367 (tpt) REVERT: B 481 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8772 (p) REVERT: B 511 GLN cc_start: 0.7393 (pt0) cc_final: 0.7086 (pm20) REVERT: B 805 LYS cc_start: 0.7953 (tppt) cc_final: 0.7723 (ttpt) REVERT: B 841 ASP cc_start: 0.6595 (OUTLIER) cc_final: 0.6023 (p0) REVERT: B 946 ASP cc_start: 0.8022 (m-30) cc_final: 0.7525 (m-30) REVERT: B 1007 TYR cc_start: 0.8475 (t80) cc_final: 0.7877 (t80) REVERT: B 1033 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.7059 (m-10) REVERT: B 1133 MET cc_start: 0.5184 (tmt) cc_final: 0.4972 (mpp) REVERT: C 134 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7476 (tm) REVERT: D 23 HIS cc_start: 0.5468 (OUTLIER) cc_final: 0.4997 (m170) REVERT: D 37 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.4859 (pp) REVERT: D 38 GLN cc_start: 0.6301 (tp-100) cc_final: 0.5136 (mp10) REVERT: E 135 PHE cc_start: 0.7396 (m-80) cc_final: 0.7009 (m-10) REVERT: E 137 GLU cc_start: 0.7202 (pt0) cc_final: 0.6878 (pt0) REVERT: E 143 ASN cc_start: 0.8496 (t0) cc_final: 0.8198 (t0) REVERT: E 163 GLU cc_start: 0.7189 (pt0) cc_final: 0.6828 (tp30) REVERT: E 179 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8145 (tp40) REVERT: G 56 ASN cc_start: 0.5935 (OUTLIER) cc_final: 0.5156 (p0) REVERT: G 59 GLN cc_start: 0.7809 (tt0) cc_final: 0.6857 (mp10) REVERT: G 90 LEU cc_start: 0.8019 (mp) cc_final: 0.7332 (mp) REVERT: G 123 TYR cc_start: 0.7681 (m-80) cc_final: 0.7464 (m-80) REVERT: H 27 GLU cc_start: 0.6764 (mp0) cc_final: 0.6519 (mp0) REVERT: H 97 MET cc_start: 0.7939 (ttm) cc_final: 0.7713 (ttm) REVERT: I 2 SER cc_start: 0.7897 (m) cc_final: 0.7650 (t) REVERT: J 49 MET cc_start: 0.9055 (mmm) cc_final: 0.8596 (mmm) REVERT: J 64 ASN cc_start: 0.8180 (t0) cc_final: 0.7594 (t0) REVERT: K 67 GLU cc_start: 0.6616 (pp20) cc_final: 0.5877 (pp20) REVERT: K 68 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8320 (mm-30) REVERT: K 69 ASP cc_start: 0.8535 (t0) cc_final: 0.8166 (t0) REVERT: K 114 VAL cc_start: 0.7723 (p) cc_final: 0.7481 (t) REVERT: K 128 CYS cc_start: 0.7477 (p) cc_final: 0.7129 (p) REVERT: M 53 LEU cc_start: 0.6470 (tt) cc_final: 0.5264 (mt) REVERT: N 107 MET cc_start: 0.5604 (OUTLIER) cc_final: 0.3944 (mpp) outliers start: 205 outliers final: 142 residues processed: 695 average time/residue: 0.1983 time to fit residues: 231.0706 Evaluate side-chains 656 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 501 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1616 GLU Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1619 CYS Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 420 TYR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 463 TYR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 841 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1015 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 13 CYS Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 95 HIS Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 160 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 409 optimal weight: 6.9990 chunk 212 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 336 optimal weight: 1.9990 chunk 398 optimal weight: 30.0000 chunk 231 optimal weight: 7.9990 chunk 201 optimal weight: 0.2980 chunk 194 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 316 optimal weight: 6.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1088 HIS ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 646 HIS ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN B1165 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.166033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139918 restraints weight = 70388.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142350 restraints weight = 42159.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.143980 restraints weight = 29703.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.145003 restraints weight = 23723.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.145505 restraints weight = 20590.415| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 34887 Z= 0.197 Angle : 0.780 24.438 47340 Z= 0.387 Chirality : 0.048 0.309 5292 Planarity : 0.005 0.059 5936 Dihedral : 11.919 86.682 5112 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.43 % Favored : 90.50 % Rotamer: Outliers : 5.80 % Allowed : 21.90 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.13), residues: 4093 helix: -0.84 (0.14), residues: 1223 sheet: -1.78 (0.22), residues: 544 loop : -2.12 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 434 TYR 0.038 0.002 TYR A 697 PHE 0.032 0.002 PHE A1535 TRP 0.013 0.002 TRP B 611 HIS 0.008 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (34863) covalent geometry : angle 0.76578 / 0.39 (47313) hydrogen bonds : bond 0.04385 / 2.91 ( 1105) hydrogen bonds : angle 6.05981 / 4.16 ( 3058) metal coordination : bond 0.01282 / 0.77 ( 23) metal coordination : angle 6.30550 / 3.56 ( 27) Misc. bond : bond 0.00225 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 535 time to evaluate : 1.548 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 15 ASP cc_start: 0.6565 (t0) cc_final: 0.5884 (m-30) REVERT: A 24 ILE cc_start: 0.8084 (pt) cc_final: 0.7841 (tp) REVERT: A 226 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.6917 (mmmt) REVERT: A 390 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 604 LYS cc_start: 0.7673 (mmmt) cc_final: 0.7246 (tptp) REVERT: A 756 LYS cc_start: 0.6802 (OUTLIER) cc_final: 0.6335 (tmtt) REVERT: A 772 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7735 (tppt) REVERT: A 946 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8256 (tm) REVERT: A 977 MET cc_start: 0.7766 (ttt) cc_final: 0.7454 (ttt) REVERT: A 997 PHE cc_start: 0.7327 (m-80) cc_final: 0.6991 (m-80) REVERT: A 1146 SER cc_start: 0.9059 (m) cc_final: 0.8363 (t) REVERT: A 1223 ARG cc_start: 0.8133 (tmm160) cc_final: 0.7717 (tmt170) REVERT: A 1227 MET cc_start: 0.7988 (mpt) cc_final: 0.7612 (mpt) REVERT: A 1238 MET cc_start: 0.8153 (mtm) cc_final: 0.7834 (ptp) REVERT: A 1535 PHE cc_start: 0.7274 (m-10) cc_final: 0.6792 (m-10) REVERT: A 1553 TYR cc_start: 0.8303 (m-80) cc_final: 0.7955 (m-80) REVERT: A 1575 ILE cc_start: 0.8259 (pp) cc_final: 0.7965 (tp) REVERT: A 1592 GLN cc_start: 0.7512 (tm-30) cc_final: 0.6902 (tm-30) REVERT: A 1611 MET cc_start: 0.7290 (mmm) cc_final: 0.6858 (tpp) REVERT: B 46 ILE cc_start: 0.8029 (mm) cc_final: 0.7239 (pt) REVERT: B 306 LEU cc_start: 0.7406 (pp) cc_final: 0.7166 (tp) REVERT: B 473 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 481 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8780 (p) REVERT: B 511 GLN cc_start: 0.7475 (pt0) cc_final: 0.7099 (pm20) REVERT: B 512 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6587 (tt) REVERT: B 773 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.7877 (t) REVERT: B 805 LYS cc_start: 0.8037 (tppt) cc_final: 0.7738 (ttpt) REVERT: B 841 ASP cc_start: 0.6654 (OUTLIER) cc_final: 0.6069 (p0) REVERT: B 950 ASN cc_start: 0.7326 (OUTLIER) cc_final: 0.7051 (m-40) REVERT: B 1007 TYR cc_start: 0.8484 (t80) cc_final: 0.7785 (t80) REVERT: B 1033 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.7209 (m-10) REVERT: B 1133 MET cc_start: 0.5175 (tmt) cc_final: 0.4972 (mpp) REVERT: C 134 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7379 (tm) REVERT: D 23 HIS cc_start: 0.5547 (OUTLIER) cc_final: 0.5001 (m170) REVERT: D 37 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.5244 (pp) REVERT: D 38 GLN cc_start: 0.6525 (tp-100) cc_final: 0.5243 (mp10) REVERT: E 135 PHE cc_start: 0.7377 (m-80) cc_final: 0.6929 (m-10) REVERT: E 137 GLU cc_start: 0.7250 (pt0) cc_final: 0.6950 (pt0) REVERT: E 143 ASN cc_start: 0.8543 (t0) cc_final: 0.8247 (t0) REVERT: G 22 LYS cc_start: 0.3983 (OUTLIER) cc_final: 0.2908 (tptt) REVERT: G 56 ASN cc_start: 0.6501 (OUTLIER) cc_final: 0.5584 (p0) REVERT: G 59 GLN cc_start: 0.7907 (tt0) cc_final: 0.6850 (mp10) REVERT: G 90 LEU cc_start: 0.8030 (mp) cc_final: 0.7505 (mp) REVERT: G 123 TYR cc_start: 0.7853 (m-80) cc_final: 0.7609 (m-80) REVERT: H 27 GLU cc_start: 0.6976 (mp0) cc_final: 0.6648 (mp0) REVERT: H 146 ARG cc_start: 0.4636 (OUTLIER) cc_final: 0.4341 (pmt-80) REVERT: I 2 SER cc_start: 0.7906 (m) cc_final: 0.7614 (t) REVERT: J 49 MET cc_start: 0.9185 (mmm) cc_final: 0.8784 (mmt) REVERT: J 64 ASN cc_start: 0.8577 (t0) cc_final: 0.8297 (t0) REVERT: K 67 GLU cc_start: 0.6478 (pp20) cc_final: 0.5716 (pp20) REVERT: K 68 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8322 (mm-30) REVERT: K 69 ASP cc_start: 0.8644 (t0) cc_final: 0.8356 (t0) REVERT: K 122 LYS cc_start: 0.8195 (tppt) cc_final: 0.7843 (ttpp) REVERT: K 128 CYS cc_start: 0.7591 (p) cc_final: 0.7212 (p) REVERT: M 53 LEU cc_start: 0.6400 (tt) cc_final: 0.5190 (mt) REVERT: N 107 MET cc_start: 0.5686 (OUTLIER) cc_final: 0.4027 (mpp) outliers start: 214 outliers final: 154 residues processed: 695 average time/residue: 0.1918 time to fit residues: 224.9723 Evaluate side-chains 668 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 496 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1616 GLU Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1619 CYS Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 420 TYR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 463 TYR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 719 CYS Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 841 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1015 SER Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 13 CYS Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 95 HIS Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 160 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 100 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 219 optimal weight: 10.0000 chunk 321 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 269 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 384 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 overall best weight: 1.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1088 HIS ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1662 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 646 HIS ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 HIS E 54 GLN G 23 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN G 65 HIS G 121 ASN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.168223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.142124 restraints weight = 69811.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.144700 restraints weight = 41029.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.146417 restraints weight = 28462.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.147368 restraints weight = 22416.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.148183 restraints weight = 19489.318| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34887 Z= 0.145 Angle : 0.761 18.910 47340 Z= 0.374 Chirality : 0.047 0.269 5292 Planarity : 0.005 0.061 5936 Dihedral : 11.870 85.829 5112 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.38 % Favored : 91.57 % Rotamer: Outliers : 4.80 % Allowed : 23.56 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.13), residues: 4093 helix: -0.77 (0.14), residues: 1247 sheet: -1.66 (0.22), residues: 550 loop : -2.04 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1444 TYR 0.039 0.002 TYR A 697 PHE 0.023 0.002 PHE A1535 TRP 0.015 0.001 TRP N 54 HIS 0.009 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (34863) covalent geometry : angle 0.74932 / 0.37 (47313) hydrogen bonds : bond 0.04144 / 2.76 ( 1105) hydrogen bonds : angle 5.89517 / 4.04 ( 3058) metal coordination : bond 0.01244 / 0.71 ( 23) metal coordination : angle 5.59058 / 3.38 ( 27) Misc. bond : bond 0.00227 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 550 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.6404 (t0) cc_final: 0.5742 (m-30) REVERT: A 24 ILE cc_start: 0.7831 (pt) cc_final: 0.7518 (tp) REVERT: A 390 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8786 (mm) REVERT: A 604 LYS cc_start: 0.7879 (mmmt) cc_final: 0.7405 (tptp) REVERT: A 635 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7410 (ttt) REVERT: A 756 LYS cc_start: 0.6591 (OUTLIER) cc_final: 0.6228 (tmtt) REVERT: A 772 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7639 (tppt) REVERT: A 960 MET cc_start: 0.5649 (mmt) cc_final: 0.5416 (mmt) REVERT: A 977 MET cc_start: 0.7671 (ttt) cc_final: 0.7318 (ttt) REVERT: A 997 PHE cc_start: 0.7242 (m-80) cc_final: 0.6884 (m-80) REVERT: A 1000 MET cc_start: 0.7561 (mtm) cc_final: 0.7092 (mtm) REVERT: A 1146 SER cc_start: 0.9005 (m) cc_final: 0.8027 (t) REVERT: A 1223 ARG cc_start: 0.8115 (tmm160) cc_final: 0.7770 (tmt170) REVERT: A 1227 MET cc_start: 0.7983 (mpt) cc_final: 0.7564 (mpt) REVERT: A 1238 MET cc_start: 0.7978 (mtm) cc_final: 0.7768 (ptp) REVERT: B 46 ILE cc_start: 0.8042 (mm) cc_final: 0.7163 (pt) REVERT: B 306 LEU cc_start: 0.7398 (pp) cc_final: 0.7174 (tp) REVERT: B 473 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7643 (tm-30) REVERT: B 481 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8754 (p) REVERT: B 511 GLN cc_start: 0.7481 (pt0) cc_final: 0.7070 (pm20) REVERT: B 512 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6634 (tt) REVERT: B 773 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.7809 (t) REVERT: B 805 LYS cc_start: 0.7937 (tppt) cc_final: 0.7677 (ttpt) REVERT: B 841 ASP cc_start: 0.6620 (OUTLIER) cc_final: 0.6060 (p0) REVERT: B 1007 TYR cc_start: 0.8506 (t80) cc_final: 0.7748 (t80) REVERT: B 1033 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.7377 (m-10) REVERT: B 1180 PHE cc_start: 0.8514 (t80) cc_final: 0.8261 (t80) REVERT: D 23 HIS cc_start: 0.5374 (OUTLIER) cc_final: 0.4565 (m-70) REVERT: D 37 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.5168 (pp) REVERT: D 38 GLN cc_start: 0.6545 (tp-100) cc_final: 0.5272 (mp10) REVERT: E 135 PHE cc_start: 0.7308 (m-80) cc_final: 0.6802 (m-10) REVERT: E 137 GLU cc_start: 0.7102 (pt0) cc_final: 0.6783 (pt0) REVERT: E 143 ASN cc_start: 0.8504 (t0) cc_final: 0.8272 (t0) REVERT: E 179 GLN cc_start: 0.8544 (tp-100) cc_final: 0.8330 (mt0) REVERT: G 22 LYS cc_start: 0.4180 (OUTLIER) cc_final: 0.3123 (tptt) REVERT: G 40 ARG cc_start: 0.5725 (mmm-85) cc_final: 0.5491 (mmm-85) REVERT: G 90 LEU cc_start: 0.8130 (mp) cc_final: 0.7747 (mp) REVERT: H 27 GLU cc_start: 0.7080 (mp0) cc_final: 0.6799 (mp0) REVERT: H 146 ARG cc_start: 0.4513 (OUTLIER) cc_final: 0.4274 (pmt-80) REVERT: J 1 MET cc_start: 0.5874 (OUTLIER) cc_final: 0.5378 (tmt) REVERT: J 49 MET cc_start: 0.9133 (mmm) cc_final: 0.8696 (mmt) REVERT: J 64 ASN cc_start: 0.8539 (t0) cc_final: 0.8267 (t0) REVERT: K 67 GLU cc_start: 0.6481 (pp20) cc_final: 0.5630 (pp20) REVERT: K 68 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8363 (mm-30) REVERT: K 69 ASP cc_start: 0.8588 (t0) cc_final: 0.8287 (t0) REVERT: K 122 LYS cc_start: 0.8054 (tppt) cc_final: 0.7806 (ttpp) REVERT: K 128 CYS cc_start: 0.7445 (p) cc_final: 0.7143 (p) REVERT: M 53 LEU cc_start: 0.6334 (tt) cc_final: 0.5101 (mt) REVERT: N 107 MET cc_start: 0.5803 (OUTLIER) cc_final: 0.4285 (mpp) outliers start: 177 outliers final: 131 residues processed: 675 average time/residue: 0.2012 time to fit residues: 227.9522 Evaluate side-chains 654 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 508 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1616 GLU Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1619 CYS Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1662 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 420 TYR Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 463 TYR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 648 ARG Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 841 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 1015 SER Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 13 CYS Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 95 HIS Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 160 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 388 optimal weight: 9.9990 chunk 397 optimal weight: 0.7980 chunk 150 optimal weight: 0.0000 chunk 307 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 345 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 356 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1592 GLN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 646 HIS ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN B1165 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 HIS G 23 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.167093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.140967 restraints weight = 69990.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.143560 restraints weight = 40638.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.145281 restraints weight = 28099.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.146388 restraints weight = 22070.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.146964 restraints weight = 18957.118| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34887 Z= 0.171 Angle : 0.782 18.082 47340 Z= 0.385 Chirality : 0.048 0.271 5292 Planarity : 0.005 0.060 5936 Dihedral : 11.888 86.314 5111 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.80 % Favored : 91.16 % Rotamer: Outliers : 5.10 % Allowed : 23.42 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.13), residues: 4093 helix: -0.71 (0.14), residues: 1248 sheet: -1.58 (0.22), residues: 543 loop : -2.01 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 25 TYR 0.030 0.002 TYR G 123 PHE 0.027 0.002 PHE E 96 TRP 0.014 0.001 TRP N 54 HIS 0.025 0.001 HIS G 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (34863) covalent geometry : angle 0.77112 / 0.38 (47313) hydrogen bonds : bond 0.04177 / 2.79 ( 1105) hydrogen bonds : angle 5.92099 / 4.07 ( 3058) metal coordination : bond 0.01103 / 0.60 ( 23) metal coordination : angle 5.51484 / 3.37 ( 27) Misc. bond : bond 0.00225 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 523 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.6457 (t0) cc_final: 0.5775 (m-30) REVERT: A 24 ILE cc_start: 0.7873 (pt) cc_final: 0.7539 (tp) REVERT: A 382 GLN cc_start: 0.7627 (mt0) cc_final: 0.7400 (mm110) REVERT: A 390 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8805 (mm) REVERT: A 604 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7327 (tptp) REVERT: A 635 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7396 (ttt) REVERT: A 756 LYS cc_start: 0.6697 (OUTLIER) cc_final: 0.6332 (tmtt) REVERT: A 772 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7356 (tppt) REVERT: A 977 MET cc_start: 0.7741 (ttt) cc_final: 0.7379 (ttt) REVERT: A 997 PHE cc_start: 0.7315 (m-80) cc_final: 0.6925 (m-80) REVERT: A 1047 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.6663 (mp10) REVERT: A 1146 SER cc_start: 0.9104 (m) cc_final: 0.8204 (t) REVERT: A 1223 ARG cc_start: 0.8088 (tmm160) cc_final: 0.7794 (tmt170) REVERT: A 1227 MET cc_start: 0.7991 (mpt) cc_final: 0.7605 (mpt) REVERT: A 1611 MET cc_start: 0.7682 (mmm) cc_final: 0.6577 (mmm) REVERT: B 46 ILE cc_start: 0.7942 (mm) cc_final: 0.7010 (pt) REVERT: B 306 LEU cc_start: 0.7453 (pp) cc_final: 0.7185 (tp) REVERT: B 461 MET cc_start: 0.8304 (mmp) cc_final: 0.8076 (mmp) REVERT: B 473 GLN cc_start: 0.7988 (tm-30) cc_final: 0.7666 (tm-30) REVERT: B 481 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8785 (p) REVERT: B 511 GLN cc_start: 0.7498 (pt0) cc_final: 0.7097 (pm20) REVERT: B 512 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6687 (tt) REVERT: B 773 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.7848 (t) REVERT: B 805 LYS cc_start: 0.7989 (tppt) cc_final: 0.7693 (ttpt) REVERT: B 841 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.6082 (p0) REVERT: B 1007 TYR cc_start: 0.8525 (t80) cc_final: 0.7763 (t80) REVERT: B 1033 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7324 (m-10) REVERT: B 1080 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7641 (tp) REVERT: B 1180 PHE cc_start: 0.8517 (t80) cc_final: 0.8245 (t80) REVERT: D 37 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.5127 (pp) REVERT: D 38 GLN cc_start: 0.6560 (tp-100) cc_final: 0.5301 (mp10) REVERT: E 135 PHE cc_start: 0.7382 (m-80) cc_final: 0.6830 (m-10) REVERT: E 137 GLU cc_start: 0.7172 (pt0) cc_final: 0.6927 (pt0) REVERT: E 143 ASN cc_start: 0.8545 (t0) cc_final: 0.8210 (t0) REVERT: E 179 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8154 (mt0) REVERT: F 57 ASP cc_start: 0.8349 (p0) cc_final: 0.7791 (p0) REVERT: F 100 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7772 (tm-30) REVERT: G 22 LYS cc_start: 0.4012 (OUTLIER) cc_final: 0.2896 (tptt) REVERT: G 62 MET cc_start: 0.6630 (tpp) cc_final: 0.6098 (mmt) REVERT: G 93 ASP cc_start: 0.7760 (p0) cc_final: 0.7500 (p0) REVERT: H 146 ARG cc_start: 0.4548 (OUTLIER) cc_final: 0.4322 (pmt-80) REVERT: J 64 ASN cc_start: 0.8612 (t0) cc_final: 0.8340 (t0) REVERT: K 67 GLU cc_start: 0.6664 (pp20) cc_final: 0.5842 (pp20) REVERT: K 68 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8357 (mm-30) REVERT: K 69 ASP cc_start: 0.8621 (t0) cc_final: 0.8362 (t0) REVERT: K 128 CYS cc_start: 0.7513 (p) cc_final: 0.7170 (p) REVERT: M 53 LEU cc_start: 0.6288 (tt) cc_final: 0.5033 (mt) REVERT: N 107 MET cc_start: 0.5882 (OUTLIER) cc_final: 0.4356 (mpp) REVERT: N 175 TYR cc_start: 0.2142 (OUTLIER) cc_final: 0.1683 (p90) outliers start: 188 outliers final: 150 residues processed: 660 average time/residue: 0.2042 time to fit residues: 227.8397 Evaluate side-chains 668 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 502 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1616 GLU Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1619 CYS Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 TYR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 463 TYR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 648 ARG Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 841 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 1015 SER Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 13 CYS Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 95 HIS Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 175 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 48 optimal weight: 0.0870 chunk 375 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 361 optimal weight: 10.0000 chunk 402 optimal weight: 20.0000 chunk 352 optimal weight: 8.9990 chunk 365 optimal weight: 6.9990 chunk 201 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 overall best weight: 3.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 ASN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1662 ASN B 267 ASN B 547 HIS B 646 HIS ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 216 HIS ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.165032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139676 restraints weight = 70984.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141799 restraints weight = 42844.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142625 restraints weight = 31339.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.143615 restraints weight = 25299.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.143674 restraints weight = 22011.768| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 34887 Z= 0.203 Angle : 0.815 17.978 47340 Z= 0.405 Chirality : 0.049 0.271 5292 Planarity : 0.005 0.061 5936 Dihedral : 11.969 86.478 5111 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.70 % Favored : 90.23 % Rotamer: Outliers : 4.91 % Allowed : 23.91 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.13), residues: 4093 helix: -0.74 (0.14), residues: 1238 sheet: -1.61 (0.22), residues: 530 loop : -2.01 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 25 TYR 0.031 0.002 TYR F 88 PHE 0.029 0.002 PHE A 920 TRP 0.020 0.002 TRP A 679 HIS 0.009 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (34863) covalent geometry : angle 0.80367 / 0.40 (47313) hydrogen bonds : bond 0.04369 / 2.90 ( 1105) hydrogen bonds : angle 5.96787 / 4.10 ( 3058) metal coordination : bond 0.01171 / 0.64 ( 23) metal coordination : angle 5.75201 / 3.47 ( 27) Misc. bond : bond 0.00228 / 0.12 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8186 Ramachandran restraints generated. 4093 Oldfield, 0 Emsley, 4093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 516 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7345 (tp30) cc_final: 0.7100 (mt-10) REVERT: A 15 ASP cc_start: 0.6474 (t0) cc_final: 0.5847 (m-30) REVERT: A 24 ILE cc_start: 0.8193 (pt) cc_final: 0.7979 (tp) REVERT: A 382 GLN cc_start: 0.7765 (mt0) cc_final: 0.7506 (mm110) REVERT: A 390 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8801 (mm) REVERT: A 604 LYS cc_start: 0.7841 (mmmt) cc_final: 0.7344 (tptp) REVERT: A 635 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7617 (ttt) REVERT: A 772 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7841 (tptt) REVERT: A 977 MET cc_start: 0.7768 (ttt) cc_final: 0.7354 (ttt) REVERT: A 1047 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.6606 (mp10) REVERT: A 1146 SER cc_start: 0.9102 (m) cc_final: 0.8333 (t) REVERT: A 1223 ARG cc_start: 0.8129 (tmm160) cc_final: 0.7817 (tmt170) REVERT: A 1227 MET cc_start: 0.8061 (mpt) cc_final: 0.7753 (mpt) REVERT: A 1485 MET cc_start: 0.5509 (mmm) cc_final: 0.5220 (mmm) REVERT: A 1553 TYR cc_start: 0.8335 (m-80) cc_final: 0.7974 (m-80) REVERT: A 1611 MET cc_start: 0.7742 (mmm) cc_final: 0.6713 (mmm) REVERT: B 46 ILE cc_start: 0.8040 (mm) cc_final: 0.7268 (pt) REVERT: B 306 LEU cc_start: 0.7484 (pp) cc_final: 0.7111 (tp) REVERT: B 461 MET cc_start: 0.8321 (mmp) cc_final: 0.8095 (mmp) REVERT: B 480 GLN cc_start: 0.7710 (pt0) cc_final: 0.7485 (pt0) REVERT: B 481 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8804 (p) REVERT: B 511 GLN cc_start: 0.8049 (pt0) cc_final: 0.7543 (pm20) REVERT: B 512 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6778 (tt) REVERT: B 672 MET cc_start: 0.7814 (ppp) cc_final: 0.7077 (ppp) REVERT: B 773 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.7911 (t) REVERT: B 805 LYS cc_start: 0.8019 (tppt) cc_final: 0.7749 (ttpt) REVERT: B 841 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6105 (p0) REVERT: B 1007 TYR cc_start: 0.8542 (t80) cc_final: 0.7771 (t80) REVERT: B 1033 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.7328 (m-10) REVERT: B 1080 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7642 (tp) REVERT: B 1180 PHE cc_start: 0.8470 (t80) cc_final: 0.8260 (t80) REVERT: D 37 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.5109 (pp) REVERT: D 38 GLN cc_start: 0.6436 (tp-100) cc_final: 0.5230 (mp10) REVERT: E 137 GLU cc_start: 0.7319 (pt0) cc_final: 0.7077 (pt0) REVERT: E 143 ASN cc_start: 0.8594 (t0) cc_final: 0.8285 (t0) REVERT: E 179 GLN cc_start: 0.8537 (tp-100) cc_final: 0.8188 (mt0) REVERT: F 61 HIS cc_start: 0.6759 (m-70) cc_final: 0.6519 (m90) REVERT: G 22 LYS cc_start: 0.4123 (OUTLIER) cc_final: 0.2830 (tptt) REVERT: G 62 MET cc_start: 0.6448 (tpp) cc_final: 0.5956 (mmm) REVERT: G 90 LEU cc_start: 0.8506 (mp) cc_final: 0.8304 (mp) REVERT: H 27 GLU cc_start: 0.7384 (mp0) cc_final: 0.7078 (pm20) REVERT: H 146 ARG cc_start: 0.4585 (OUTLIER) cc_final: 0.4355 (pmt-80) REVERT: J 64 ASN cc_start: 0.8671 (t0) cc_final: 0.8389 (t0) REVERT: K 67 GLU cc_start: 0.6791 (pp20) cc_final: 0.6031 (pp20) REVERT: K 68 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8244 (mm-30) REVERT: K 69 ASP cc_start: 0.8658 (t0) cc_final: 0.8380 (t0) REVERT: K 128 CYS cc_start: 0.7473 (p) cc_final: 0.7157 (p) REVERT: L 57 LEU cc_start: 0.8323 (mm) cc_final: 0.8064 (mp) REVERT: M 52 VAL cc_start: 0.6835 (OUTLIER) cc_final: 0.6576 (t) REVERT: M 53 LEU cc_start: 0.6334 (tt) cc_final: 0.5135 (mt) REVERT: N 107 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.4430 (mpp) REVERT: N 175 TYR cc_start: 0.2260 (OUTLIER) cc_final: 0.1765 (p90) outliers start: 181 outliers final: 153 residues processed: 649 average time/residue: 0.2065 time to fit residues: 225.4738 Evaluate side-chains 663 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 494 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1616 GLU Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1619 CYS Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1662 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 TYR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 463 TYR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 648 ARG Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 841 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 1015 SER Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 13 CYS Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 95 HIS Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 175 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 109 optimal weight: 3.9990 chunk 179 optimal weight: 0.0370 chunk 287 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 208 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 overall best weight: 2.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN B 547 HIS B 646 HIS ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 GLN B 767 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.166353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141028 restraints weight = 70100.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.143254 restraints weight = 42298.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.144181 restraints weight = 30364.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.145049 restraints weight = 24618.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.145157 restraints weight = 21397.803| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 34887 Z= 0.166 Angle : 0.803 19.916 47340 Z= 0.393 Chirality : 0.047 0.262 5292 Planarity : 0.005 0.061 5936 Dihedral : 11.948 85.854 5111 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.02 % Favored : 90.91 % Rotamer: Outliers : 4.91 % Allowed : 24.13 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.13), residues: 4093 helix: -0.67 (0.14), residues: 1241 sheet: -1.56 (0.22), residues: 535 loop : -1.99 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 47 TYR 0.034 0.002 TYR A 697 PHE 0.035 0.002 PHE A 920 TRP 0.017 0.002 TRP B 143 HIS 0.010 0.001 HIS F 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (34863) covalent geometry : angle 0.78354 / 0.39 (47313) hydrogen bonds : bond 0.04193 / 2.80 ( 1105) hydrogen bonds : angle 5.89331 / 4.05 ( 3058) metal coordination : bond 0.01883 / 1.29 ( 23) metal coordination : angle 7.38356 / 4.03 ( 27) Misc. bond : bond 0.00230 / 0.12 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6693.10 seconds wall clock time: 116 minutes 53.52 seconds (7013.52 seconds total)