Starting phenix.real_space_refine on Tue Aug 26 05:56:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5m5y_3448/08_2025/5m5y_3448_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5m5y_3448/08_2025/5m5y_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_3448/08_2025/5m5y_3448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5m5y_3448/08_2025/5m5y_3448.map" model { file = "/net/cci-nas-00/data/ceres_data/5m5y_3448/08_2025/5m5y_3448_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5m5y_3448/08_2025/5m5y_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-2.0-5787/lib/python3.9/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: 7.33, 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: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3.24 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: 8.55 Time building geometry restraints manager: 3.77 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 36.110 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 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= 0.205 Angle : 0.870 45.464 47340 Z= 0.415 Chirality : 0.050 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 aren 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 covalent geometry : bond 0.00256 (34863) covalent geometry : angle 0.69048 (47313) hydrogen bonds : bond 0.21273 ( 1105) hydrogen bonds : angle 10.46290 ( 3058) metal coordination : bond 0.14938 ( 23) metal coordination : angle 22.16360 ( 27) Misc. bond : bond 0.04514 ( 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 : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.4354 (t) REVERT: A 594 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8575 (t) REVERT: A 613 THR cc_start: 0.7146 (m) cc_final: 0.6669 (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: 0.5960 (mmt) REVERT: A 1027 LEU cc_start: 0.8109 (tp) cc_final: 0.7623 (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: 0.8725 (m) REVERT: A 1223 ARG cc_start: 0.7775 (tmm160) cc_final: 0.7435 (tmt170) REVERT: A 1228 THR cc_start: 0.6715 (p) cc_final: 0.6422 (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: 0.7859 (mtpt) REVERT: B 22 GLU cc_start: 0.7448 (tp30) cc_final: 0.6796 (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: 0.7703 (pp) REVERT: B 164 MET cc_start: 0.7325 (pmm) cc_final: 0.6892 (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: 0.6033 (mmp) REVERT: B 359 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5350 (tt) REVERT: B 549 CYS cc_start: 0.7532 (p) cc_final: 0.7289 (p) REVERT: B 606 ASP cc_start: 0.7450 (p0) cc_final: 0.7155 (p0) REVERT: B 841 ASP cc_start: 0.6584 (m-30) cc_final: 0.6216 (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: 0.4491 (mpp) REVERT: B 1186 ASP cc_start: 0.7282 (p0) cc_final: 0.6927 (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: 0.8470 (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: 0.5227 (mp10) REVERT: E 135 PHE cc_start: 0.7673 (m-80) cc_final: 0.7255 (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: 0.7275 (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: 0.6362 (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: 0.1352 (p0) REVERT: G 59 GLN cc_start: 0.6990 (tt0) cc_final: 0.6338 (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: 0.6656 (t) REVERT: J 62 ARG cc_start: 0.6973 (mmm-85) cc_final: 0.6727 (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: 0.6759 (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: 0.5342 (mmmt) REVERT: M 86 LYS cc_start: 0.5236 (mmtm) cc_final: 0.4839 (pttm) REVERT: N 40 LEU cc_start: 0.5564 (tm) cc_final: 0.5363 (pp) outliers start: 61 outliers final: 10 residues processed: 1183 average time/residue: 0.2470 time to fit residues: 461.2855 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 : 1.430 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN A 798 HIS A 926 GLN A 998 HIS A1072 ASN 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 A1620 GLN B 62 ASN B 87 ASN B 231 HIS B 243 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 ASN ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN C 99 HIS C 130 ASN C 216 HIS C 301 ASN 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: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.177534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.151789 restraints weight = 70028.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.154592 restraints weight = 40621.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.156446 restraints weight = 27640.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.157621 restraints weight = 21451.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.158406 restraints weight = 18264.572| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2697 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= 0.158 Angle : 0.766 32.497 47340 Z= 0.374 Chirality : 0.046 0.315 5292 Planarity : 0.005 0.073 5936 Dihedral : 11.613 89.888 5129 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 4.45 % Allowed : 17.19 % Favored : 78.37 % 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 aren not related in a simple way. whole: -3.30 (0.12), residues: 4093 helix: -1.97 (0.13), residues: 1209 sheet: -1.85 (0.21), residues: 522 loop : -2.46 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1063 TYR 0.027 0.002 TYR A 618 PHE 0.028 0.002 PHE A 91 TRP 0.038 0.002 TRP B 984 HIS 0.009 0.001 HIS B 547 Details of bonding type rmsd covalent geometry : bond 0.00356 (34863) covalent geometry : angle 0.73253 (47313) hydrogen bonds : bond 0.04954 ( 1105) hydrogen bonds : angle 6.91038 ( 3058) metal coordination : bond 0.01376 ( 23) metal coordination : angle 9.46258 ( 27) Misc. bond : bond 0.00183 ( 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 850 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 686 time to evaluate : 1.233 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: A 24 ILE cc_start: 0.7899 (pt) cc_final: 0.7352 (tp) REVERT: A 221 HIS cc_start: 0.7162 (t-90) cc_final: 0.6805 (t-90) REVERT: A 225 LYS cc_start: 0.6687 (pptt) cc_final: 0.6350 (mmtt) REVERT: A 260 GLN cc_start: 0.7817 (mt0) cc_final: 0.7588 (mt0) REVERT: A 464 GLU cc_start: 0.4823 (tm-30) cc_final: 0.4605 (tm-30) REVERT: A 528 ASP cc_start: 0.8473 (p0) cc_final: 0.8222 (p0) REVERT: A 594 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8619 (t) REVERT: A 633 MET cc_start: 0.8011 (ttm) cc_final: 0.7805 (ttm) REVERT: A 772 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7774 (tppt) REVERT: A 786 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6514 (t80) REVERT: A 937 ASN cc_start: 0.6854 (t0) cc_final: 0.6632 (t0) REVERT: A 946 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7588 (tm) REVERT: A 960 MET cc_start: 0.5607 (mmt) cc_final: 0.5336 (mmt) REVERT: A 1000 MET cc_start: 0.7896 (mtm) cc_final: 0.7545 (mtm) REVERT: A 1049 MET cc_start: 0.6764 (mtp) cc_final: 0.6401 (mtm) REVERT: A 1146 SER cc_start: 0.9043 (m) cc_final: 0.8119 (t) REVERT: A 1223 ARG cc_start: 0.7868 (tmm160) cc_final: 0.7579 (tmt170) REVERT: A 1441 LYS cc_start: 0.7048 (tptt) cc_final: 0.6776 (tttm) REVERT: A 1566 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8022 (mt) REVERT: B 46 ILE cc_start: 0.7945 (mm) cc_final: 0.7415 (pt) REVERT: B 181 VAL cc_start: 0.9207 (t) cc_final: 0.8889 (m) REVERT: B 205 MET cc_start: 0.8068 (mmm) cc_final: 0.7686 (mtt) REVERT: B 275 MET cc_start: 0.6277 (mpm) cc_final: 0.5895 (mmp) REVERT: B 450 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8446 (tt) REVERT: B 473 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7385 (tm-30) REVERT: B 481 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8723 (p) REVERT: B 668 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6635 (tm-30) REVERT: B 672 MET cc_start: 0.7491 (ppp) cc_final: 0.6904 (ppp) REVERT: B 765 PHE cc_start: 0.7956 (m-80) cc_final: 0.7684 (m-80) REVERT: B 773 VAL cc_start: 0.7621 (OUTLIER) cc_final: 0.7347 (t) REVERT: B 839 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6623 (mtmt) REVERT: B 840 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6584 (mp) REVERT: B 1007 TYR cc_start: 0.8107 (t80) cc_final: 0.7776 (t80) REVERT: B 1033 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6471 (m-10) REVERT: B 1133 MET cc_start: 0.5044 (tmt) cc_final: 0.4619 (mpp) REVERT: B 1151 ILE cc_start: 0.2236 (OUTLIER) cc_final: 0.1655 (tp) REVERT: C 74 GLU cc_start: 0.7073 (pm20) cc_final: 0.6862 (pp20) REVERT: C 89 THR cc_start: 0.8779 (p) cc_final: 0.8509 (t) REVERT: D 38 GLN cc_start: 0.5647 (tp-100) cc_final: 0.4881 (mp10) REVERT: E 135 PHE cc_start: 0.7493 (m-80) cc_final: 0.7081 (m-10) REVERT: E 179 GLN cc_start: 0.8617 (tp-100) cc_final: 0.8058 (mt0) REVERT: E 182 ASP cc_start: 0.7801 (t70) cc_final: 0.7376 (t70) REVERT: E 190 LEU cc_start: 0.7757 (mt) cc_final: 0.6999 (tt) REVERT: E 211 TYR cc_start: 0.8073 (m-80) cc_final: 0.7804 (m-80) REVERT: F 86 THR cc_start: 0.7292 (p) cc_final: 0.7066 (p) REVERT: G 59 GLN cc_start: 0.7330 (tt0) cc_final: 0.6452 (mp10) REVERT: H 49 VAL cc_start: 0.6644 (t) cc_final: 0.6392 (p) REVERT: H 109 LYS cc_start: 0.8695 (tmtt) cc_final: 0.8104 (tmtt) REVERT: I 2 SER cc_start: 0.7765 (m) cc_final: 0.7363 (t) REVERT: J 49 MET cc_start: 0.8169 (mmt) cc_final: 0.7823 (mmm) REVERT: J 64 ASN cc_start: 0.7689 (t0) cc_final: 0.7051 (t0) REVERT: K 67 GLU cc_start: 0.6892 (pp20) cc_final: 0.6058 (pp20) REVERT: K 68 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8260 (mm-30) REVERT: K 122 LYS cc_start: 0.8340 (tppt) cc_final: 0.7859 (ptmm) REVERT: K 125 MET cc_start: 0.7372 (mmm) cc_final: 0.7090 (mmm) REVERT: K 128 CYS cc_start: 0.7079 (p) cc_final: 0.6866 (p) REVERT: K 133 SER cc_start: 0.8347 (m) cc_final: 0.8131 (p) REVERT: L 28 LYS cc_start: 0.5796 (pttm) cc_final: 0.5508 (mmmt) REVERT: L 64 LEU cc_start: 0.7078 (tp) cc_final: 0.6778 (tt) REVERT: M 53 LEU cc_start: 0.6456 (mt) cc_final: 0.6253 (tt) REVERT: M 86 LYS cc_start: 0.5798 (mmtm) cc_final: 0.5170 (pttm) outliers start: 164 outliers final: 65 residues processed: 807 average time/residue: 0.2267 time to fit residues: 298.4541 Evaluate side-chains 635 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 558 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 399 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 568 VAL 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 962 SER Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1135 SER 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 195 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 ILE 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 821 ILE Chi-restraints excluded: chain B residue 839 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 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 1187 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 156 LEU 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 122 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 60 PHE 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: 5.9990 chunk 121 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 376 optimal weight: 10.0000 chunk 346 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN A 671 GLN ** 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 398 GLN 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** C 216 HIS ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.169746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143332 restraints weight = 70420.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145956 restraints weight = 41307.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.147696 restraints weight = 28647.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.148839 restraints weight = 22504.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.149510 restraints weight = 19338.466| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 34887 Z= 0.216 Angle : 0.771 30.240 47340 Z= 0.385 Chirality : 0.048 0.307 5292 Planarity : 0.006 0.077 5936 Dihedral : 11.683 89.276 5115 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.11 % Favored : 91.79 % Rotamer: Outliers : 5.18 % Allowed : 18.54 % Favored : 76.28 % 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 aren not related in a simple way. whole: -2.90 (0.12), residues: 4093 helix: -1.44 (0.13), residues: 1248 sheet: -1.87 (0.21), residues: 557 loop : -2.25 (0.12), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 40 TYR 0.025 0.002 TYR A 314 PHE 0.026 0.002 PHE A1472 TRP 0.013 0.002 TRP B 611 HIS 0.029 0.002 HIS K 95 Details of bonding type rmsd covalent geometry : bond 0.00480 (34863) covalent geometry : angle 0.74785 (47313) hydrogen bonds : bond 0.04753 ( 1105) hydrogen bonds : angle 6.33373 ( 3058) metal coordination : bond 0.01146 ( 23) metal coordination : angle 7.83499 ( 27) Misc. bond : bond 0.00195 ( 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 802 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 611 time to evaluate : 1.428 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: 0.6554 (t0) cc_final: 0.5932 (m-30) REVERT: A 24 ILE cc_start: 0.8063 (pt) cc_final: 0.7817 (tp) REVERT: A 221 HIS cc_start: 0.7189 (t-90) cc_final: 0.6835 (t-90) REVERT: A 428 VAL cc_start: 0.8486 (t) cc_final: 0.8184 (p) REVERT: A 464 GLU cc_start: 0.5499 (tm-30) cc_final: 0.5201 (tm-30) REVERT: A 528 ASP cc_start: 0.8509 (p0) cc_final: 0.8291 (p0) REVERT: A 589 MET cc_start: 0.8009 (tpp) cc_final: 0.7751 (tpp) REVERT: A 756 LYS cc_start: 0.6707 (OUTLIER) cc_final: 0.6201 (tmtt) REVERT: A 765 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7522 (mm) REVERT: A 772 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7532 (tppt) REVERT: A 833 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7905 (tt) REVERT: A 937 ASN cc_start: 0.6990 (t0) cc_final: 0.6753 (t0) REVERT: A 946 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7932 (tm) REVERT: A 977 MET cc_start: 0.7552 (ttt) cc_final: 0.7136 (ttt) REVERT: A 1000 MET cc_start: 0.7850 (mtm) cc_final: 0.7345 (mtm) REVERT: A 1146 SER cc_start: 0.8938 (m) cc_final: 0.8111 (t) REVERT: A 1223 ARG cc_start: 0.7968 (tmm160) cc_final: 0.7695 (tmt170) REVERT: A 1441 LYS cc_start: 0.6918 (tptt) cc_final: 0.6604 (tttm) REVERT: A 1499 ARG cc_start: 0.6407 (OUTLIER) cc_final: 0.5915 (ptt-90) REVERT: A 1611 MET cc_start: 0.7138 (mmm) cc_final: 0.6773 (tpp) REVERT: B 46 ILE cc_start: 0.8086 (mm) cc_final: 0.7376 (pt) REVERT: B 205 MET cc_start: 0.8072 (mmm) cc_final: 0.7866 (mtt) REVERT: B 217 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6287 (mt) REVERT: B 275 MET cc_start: 0.6615 (mpm) cc_final: 0.6076 (mmp) REVERT: B 481 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8813 (p) REVERT: B 521 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7646 (tp) REVERT: B 527 PHE cc_start: 0.7482 (m-10) cc_final: 0.7157 (m-10) REVERT: B 566 TYR cc_start: 0.6847 (t80) cc_final: 0.6639 (t80) REVERT: B 672 MET cc_start: 0.7857 (ppp) cc_final: 0.7072 (ppp) REVERT: B 679 GLN cc_start: 0.8403 (mp10) cc_final: 0.7776 (mp10) REVERT: B 762 MET cc_start: 0.7824 (mpt) cc_final: 0.7580 (mmt) REVERT: B 773 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7957 (t) REVERT: B 840 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6433 (mp) REVERT: B 841 ASP cc_start: 0.6744 (m-30) cc_final: 0.6406 (p0) REVERT: B 946 ASP cc_start: 0.7908 (m-30) cc_final: 0.7463 (m-30) REVERT: B 1007 TYR cc_start: 0.8324 (t80) cc_final: 0.7979 (t80) REVERT: B 1031 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7585 (m) REVERT: B 1033 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.7070 (m-10) REVERT: B 1133 MET cc_start: 0.5264 (tmt) cc_final: 0.4751 (mpp) REVERT: B 1151 ILE cc_start: 0.2398 (OUTLIER) cc_final: 0.1590 (tp) REVERT: B 1186 ASP cc_start: 0.7551 (p0) cc_final: 0.7284 (p0) REVERT: C 100 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.8171 (ttm170) REVERT: D 23 HIS cc_start: 0.5374 (OUTLIER) cc_final: 0.4834 (m170) REVERT: D 38 GLN cc_start: 0.5960 (tp-100) cc_final: 0.4876 (mp10) REVERT: E 135 PHE cc_start: 0.7503 (m-80) cc_final: 0.6916 (m-10) REVERT: E 179 GLN cc_start: 0.8602 (tp-100) cc_final: 0.8285 (tp-100) REVERT: E 182 ASP cc_start: 0.7914 (t70) cc_final: 0.7601 (t70) REVERT: E 190 LEU cc_start: 0.7930 (mt) cc_final: 0.6990 (tt) REVERT: F 65 ARG cc_start: 0.7289 (ttp-170) cc_final: 0.7053 (ttp-170) REVERT: F 86 THR cc_start: 0.7454 (p) cc_final: 0.6736 (p) REVERT: F 89 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7062 (mt-10) REVERT: G 59 GLN cc_start: 0.7670 (tt0) cc_final: 0.6659 (mp10) REVERT: G 90 LEU cc_start: 0.8043 (mp) cc_final: 0.7517 (mp) REVERT: G 119 HIS cc_start: 0.6623 (m-70) cc_final: 0.6388 (m-70) REVERT: I 2 SER cc_start: 0.7687 (m) cc_final: 0.7367 (t) REVERT: J 49 MET cc_start: 0.8458 (mmt) cc_final: 0.8137 (mmm) REVERT: J 64 ASN cc_start: 0.8174 (t0) cc_final: 0.7486 (t0) REVERT: K 69 ASP cc_start: 0.8443 (t0) cc_final: 0.8173 (t0) REVERT: K 98 GLU cc_start: 0.6795 (pt0) cc_final: 0.6454 (pt0) REVERT: K 122 LYS cc_start: 0.8285 (tppt) cc_final: 0.7833 (ttpp) REVERT: K 125 MET cc_start: 0.7238 (mmm) cc_final: 0.6949 (mmm) REVERT: K 126 ASP cc_start: 0.8295 (m-30) cc_final: 0.8012 (m-30) REVERT: K 128 CYS cc_start: 0.7296 (p) cc_final: 0.6998 (p) REVERT: L 60 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7752 (ttm-80) REVERT: L 64 LEU cc_start: 0.7450 (tp) cc_final: 0.7151 (tt) REVERT: M 53 LEU cc_start: 0.6549 (mt) cc_final: 0.6320 (tp) REVERT: M 86 LYS cc_start: 0.6199 (mmtm) cc_final: 0.5456 (pttm) REVERT: N 40 LEU cc_start: 0.5756 (tm) cc_final: 0.5374 (pp) REVERT: N 107 MET cc_start: 0.5149 (OUTLIER) cc_final: 0.3594 (mpp) outliers start: 191 outliers final: 97 residues processed: 751 average time/residue: 0.2221 time to fit residues: 274.1879 Evaluate side-chains 623 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 510 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 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 514 TYR Chi-restraints excluded: chain A residue 550 SER 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 765 LEU 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 833 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 982 VAL 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 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 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 195 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 217 ILE 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 521 LEU 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 741 LEU Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 840 LEU 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 939 SER Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1015 SER Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR 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 104 VAL Chi-restraints excluded: chain C residue 108 VAL 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 C residue 309 THR Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 77 ASP 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 238 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 122 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 60 PHE Chi-restraints excluded: chain K residue 47 ILE 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 40 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 270 optimal weight: 0.7980 chunk 343 optimal weight: 20.0000 chunk 243 optimal weight: 9.9990 chunk 242 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 309 optimal weight: 10.0000 chunk 80 optimal weight: 0.0470 chunk 304 optimal weight: 0.2980 chunk 282 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN A 620 ASN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1072 ASN A1088 HIS A1314 GLN A1443 GLN A1581 HIS A1662 ASN B 45 HIS B 128 GLN B 168 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 ASN ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN E 54 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS G 160 ASN ** 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.171761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.145556 restraints weight = 69987.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.148159 restraints weight = 41583.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.149911 restraints weight = 28965.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.150926 restraints weight = 22837.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.151758 restraints weight = 19705.620| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3948 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= 0.141 Angle : 0.709 26.106 47340 Z= 0.349 Chirality : 0.045 0.321 5292 Planarity : 0.005 0.073 5936 Dihedral : 11.627 86.018 5113 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.06 % Favored : 92.84 % Rotamer: Outliers : 5.15 % Allowed : 19.76 % Favored : 75.09 % 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 aren not related in a simple way. whole: -2.61 (0.12), residues: 4093 helix: -1.13 (0.14), residues: 1259 sheet: -1.70 (0.21), residues: 542 loop : -2.12 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 25 TYR 0.028 0.002 TYR G 84 PHE 0.031 0.002 PHE B 667 TRP 0.030 0.002 TRP B 143 HIS 0.009 0.001 HIS B 547 Details of bonding type rmsd covalent geometry : bond 0.00321 (34863) covalent geometry : angle 0.69241 (47313) hydrogen bonds : bond 0.04165 ( 1105) hydrogen bonds : angle 5.97201 ( 3058) metal coordination : bond 0.01184 ( 23) metal coordination : angle 6.34177 ( 27) Misc. bond : bond 0.00204 ( 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 786 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 596 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.6477 (t0) cc_final: 0.5756 (m-30) REVERT: A 24 ILE cc_start: 0.7833 (pt) cc_final: 0.7493 (tp) REVERT: A 98 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8350 (mm) REVERT: A 221 HIS cc_start: 0.7173 (t-90) cc_final: 0.6840 (t-90) REVERT: A 428 VAL cc_start: 0.8466 (t) cc_final: 0.8171 (p) REVERT: A 464 GLU cc_start: 0.5292 (tm-30) cc_final: 0.5034 (tm-30) REVERT: A 471 MET cc_start: 0.8194 (mmm) cc_final: 0.7967 (mpp) REVERT: A 589 MET cc_start: 0.7910 (tpp) cc_final: 0.7615 (tpp) REVERT: A 601 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7992 (ttp) REVERT: A 744 MET cc_start: 0.7969 (tpt) cc_final: 0.7516 (mmt) REVERT: A 756 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6236 (tmtt) REVERT: A 772 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7704 (tppt) REVERT: A 810 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8382 (mt) REVERT: A 925 MET cc_start: 0.8173 (tmm) cc_final: 0.7972 (tmm) REVERT: A 937 ASN cc_start: 0.6970 (t0) cc_final: 0.6688 (t0) REVERT: A 946 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7916 (tm) REVERT: A 960 MET cc_start: 0.5870 (mmt) cc_final: 0.5392 (mmt) REVERT: A 977 MET cc_start: 0.7440 (ttt) cc_final: 0.7141 (ttt) REVERT: A 1000 MET cc_start: 0.7734 (mtm) cc_final: 0.7263 (mtm) REVERT: A 1047 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7610 (mp10) REVERT: A 1078 LYS cc_start: 0.7180 (tttt) cc_final: 0.6806 (tttt) REVERT: A 1146 SER cc_start: 0.8962 (m) cc_final: 0.8090 (t) REVERT: A 1223 ARG cc_start: 0.8086 (tmm160) cc_final: 0.7739 (tmt170) REVERT: A 1441 LYS cc_start: 0.6864 (tptt) cc_final: 0.6604 (tttm) REVERT: A 1575 ILE cc_start: 0.8136 (pp) cc_final: 0.7823 (tp) REVERT: A 1592 GLN cc_start: 0.7278 (tm-30) cc_final: 0.6941 (tm-30) REVERT: A 1611 MET cc_start: 0.7190 (mmm) cc_final: 0.6672 (tpp) REVERT: A 1613 MET cc_start: 0.7890 (mmt) cc_final: 0.7673 (mmt) REVERT: B 46 ILE cc_start: 0.8051 (mm) cc_final: 0.7216 (pt) REVERT: B 261 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7501 (ttp-170) REVERT: B 436 MET cc_start: 0.5539 (ppp) cc_final: 0.5338 (pmm) REVERT: B 481 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8782 (p) REVERT: B 566 TYR cc_start: 0.7179 (t80) cc_final: 0.6810 (t80) REVERT: B 672 MET cc_start: 0.7679 (ppp) cc_final: 0.7040 (ppp) REVERT: B 679 GLN cc_start: 0.8312 (mp10) cc_final: 0.7647 (mp10) REVERT: B 764 ASN cc_start: 0.7500 (m-40) cc_final: 0.7228 (m-40) REVERT: B 773 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7504 (t) REVERT: B 841 ASP cc_start: 0.6649 (m-30) cc_final: 0.6434 (p0) REVERT: B 935 ASP cc_start: 0.7229 (t0) cc_final: 0.6792 (t70) REVERT: B 946 ASP cc_start: 0.7957 (m-30) cc_final: 0.7554 (m-30) REVERT: B 1007 TYR cc_start: 0.8308 (t80) cc_final: 0.7855 (t80) REVERT: B 1031 VAL cc_start: 0.7766 (p) cc_final: 0.7470 (m) REVERT: B 1033 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7035 (m-10) REVERT: B 1133 MET cc_start: 0.5093 (tmt) cc_final: 0.4817 (mpp) REVERT: B 1151 ILE cc_start: 0.2440 (OUTLIER) cc_final: 0.1618 (tp) REVERT: B 1181 VAL cc_start: 0.9085 (p) cc_final: 0.8884 (p) REVERT: B 1186 ASP cc_start: 0.7550 (p0) cc_final: 0.7328 (p0) REVERT: B 1194 ILE cc_start: 0.8589 (pp) cc_final: 0.8320 (pp) REVERT: C 100 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.8098 (mmm-85) REVERT: D 23 HIS cc_start: 0.5144 (OUTLIER) cc_final: 0.4564 (m170) REVERT: D 38 GLN cc_start: 0.5926 (tp-100) cc_final: 0.4862 (mp10) REVERT: E 135 PHE cc_start: 0.7468 (m-80) cc_final: 0.6883 (m-10) REVERT: E 137 GLU cc_start: 0.7132 (pt0) cc_final: 0.6803 (pt0) REVERT: E 182 ASP cc_start: 0.7824 (t70) cc_final: 0.7573 (t70) REVERT: E 190 LEU cc_start: 0.7897 (mt) cc_final: 0.6914 (tp) REVERT: F 89 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7285 (mt-10) REVERT: G 59 GLN cc_start: 0.7435 (tt0) cc_final: 0.6718 (mp10) REVERT: G 90 LEU cc_start: 0.8028 (mp) cc_final: 0.7346 (mp) REVERT: G 119 HIS cc_start: 0.6525 (m-70) cc_final: 0.6175 (m-70) REVERT: H 7 ASP cc_start: 0.7649 (t0) cc_final: 0.7124 (p0) REVERT: I 2 SER cc_start: 0.7750 (m) cc_final: 0.7443 (t) REVERT: J 49 MET cc_start: 0.8179 (mmt) cc_final: 0.7949 (mmm) REVERT: J 64 ASN cc_start: 0.8023 (t0) cc_final: 0.7438 (t0) REVERT: K 67 GLU cc_start: 0.6762 (pp20) cc_final: 0.5739 (pp20) REVERT: K 68 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8221 (mm-30) REVERT: K 69 ASP cc_start: 0.8467 (t0) cc_final: 0.8071 (t0) REVERT: K 114 VAL cc_start: 0.7737 (p) cc_final: 0.7491 (t) REVERT: K 122 LYS cc_start: 0.8510 (tppt) cc_final: 0.8255 (ttpp) REVERT: K 125 MET cc_start: 0.7094 (mmm) cc_final: 0.6714 (tpp) REVERT: K 128 CYS cc_start: 0.7474 (p) cc_final: 0.7250 (p) REVERT: L 49 LYS cc_start: 0.5741 (mppt) cc_final: 0.5461 (ttmt) REVERT: L 64 LEU cc_start: 0.7594 (tp) cc_final: 0.7283 (tt) REVERT: N 40 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5415 (pp) REVERT: N 107 MET cc_start: 0.5311 (OUTLIER) cc_final: 0.3821 (mpp) outliers start: 190 outliers final: 102 residues processed: 735 average time/residue: 0.2139 time to fit residues: 262.8972 Evaluate side-chains 644 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 527 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 98 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 386 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 601 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 810 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 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 1047 GLN Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1179 ILE 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 1643 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain B residue 42 VAL 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 261 ARG Chi-restraints excluded: chain B residue 358 VAL 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 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 721 MET Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 787 MET 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 960 ILE 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 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 108 VAL 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 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 78 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 62 MET 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 42 PHE Chi-restraints excluded: chain I residue 48 VAL 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 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 40 LEU 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 40 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 56 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 348 optimal weight: 40.0000 chunk 399 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 370 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A1662 ASN B 45 HIS ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1165 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.170228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.144393 restraints weight = 70288.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.147167 restraints weight = 41964.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.148036 restraints weight = 29256.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.149029 restraints weight = 23671.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.149155 restraints weight = 20354.011| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34887 Z= 0.154 Angle : 0.713 23.127 47340 Z= 0.352 Chirality : 0.045 0.244 5292 Planarity : 0.005 0.073 5936 Dihedral : 11.641 85.865 5113 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.04 % Favored : 91.89 % Rotamer: Outliers : 5.39 % Allowed : 21.04 % Favored : 73.57 % 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 aren not related in a simple way. whole: -2.44 (0.13), residues: 4093 helix: -0.92 (0.14), residues: 1262 sheet: -1.67 (0.22), residues: 536 loop : -2.06 (0.13), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 60 TYR 0.026 0.002 TYR K 91 PHE 0.032 0.002 PHE A1535 TRP 0.023 0.002 TRP B 143 HIS 0.009 0.001 HIS A1454 Details of bonding type rmsd covalent geometry : bond 0.00355 (34863) covalent geometry : angle 0.69999 (47313) hydrogen bonds : bond 0.04093 ( 1105) hydrogen bonds : angle 5.82810 ( 3058) metal coordination : bond 0.01031 ( 23) metal coordination : angle 5.63669 ( 27) Misc. bond : bond 0.00211 ( 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 780 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 581 time to evaluate : 1.117 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: 0.6485 (t0) cc_final: 0.5756 (m-30) REVERT: A 24 ILE cc_start: 0.7863 (pt) cc_final: 0.7516 (tp) REVERT: A 36 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7674 (p) REVERT: A 98 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8378 (mm) REVERT: A 214 ASP cc_start: 0.7862 (t0) cc_final: 0.7458 (t0) REVERT: A 221 HIS cc_start: 0.7137 (t-90) cc_final: 0.6838 (t-90) REVERT: A 464 GLU cc_start: 0.5358 (tm-30) cc_final: 0.5074 (tm-30) REVERT: A 471 MET cc_start: 0.8600 (mmm) cc_final: 0.7744 (mpp) REVERT: A 601 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8074 (ttp) REVERT: A 756 LYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6358 (tmtt) REVERT: A 772 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7379 (tppt) REVERT: A 937 ASN cc_start: 0.7023 (t0) cc_final: 0.6735 (t0) REVERT: A 946 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8035 (tm) REVERT: A 977 MET cc_start: 0.7395 (ttt) cc_final: 0.7076 (ttt) REVERT: A 997 PHE cc_start: 0.7196 (m-80) cc_final: 0.6911 (m-80) REVERT: A 1000 MET cc_start: 0.7570 (mtm) cc_final: 0.7085 (mtm) REVERT: A 1146 SER cc_start: 0.9007 (m) cc_final: 0.8206 (t) REVERT: A 1200 MET cc_start: 0.6108 (tmm) cc_final: 0.5903 (tmm) REVERT: A 1223 ARG cc_start: 0.8157 (tmm160) cc_final: 0.7718 (tmt170) REVERT: A 1227 MET cc_start: 0.7945 (mpt) cc_final: 0.7516 (mpt) REVERT: A 1575 ILE cc_start: 0.8153 (pp) cc_final: 0.7860 (tp) REVERT: A 1611 MET cc_start: 0.7273 (mmm) cc_final: 0.6650 (tpp) REVERT: A 1615 TYR cc_start: 0.8331 (t80) cc_final: 0.8119 (t80) REVERT: B 46 ILE cc_start: 0.8166 (mm) cc_final: 0.7281 (pt) REVERT: B 205 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7625 (mtp) REVERT: B 261 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7491 (ttp-170) REVERT: B 411 MET cc_start: 0.8648 (tpp) cc_final: 0.8236 (mmt) REVERT: B 436 MET cc_start: 0.5588 (ppp) cc_final: 0.5380 (pmm) REVERT: B 473 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 481 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8774 (p) REVERT: B 566 TYR cc_start: 0.7082 (t80) cc_final: 0.6785 (t80) REVERT: B 679 GLN cc_start: 0.8365 (mp10) cc_final: 0.7660 (mp10) REVERT: B 764 ASN cc_start: 0.7224 (m-40) cc_final: 0.6957 (m-40) REVERT: B 841 ASP cc_start: 0.6500 (m-30) cc_final: 0.6139 (p0) REVERT: B 913 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8288 (mt) REVERT: B 935 ASP cc_start: 0.7233 (t0) cc_final: 0.6804 (t70) REVERT: B 946 ASP cc_start: 0.8134 (m-30) cc_final: 0.7738 (m-30) REVERT: B 947 ILE cc_start: 0.8931 (pt) cc_final: 0.8587 (mt) REVERT: B 1007 TYR cc_start: 0.8292 (t80) cc_final: 0.7743 (t80) REVERT: B 1013 MET cc_start: 0.7727 (mtp) cc_final: 0.7384 (mtt) REVERT: B 1031 VAL cc_start: 0.7747 (p) cc_final: 0.7329 (m) REVERT: B 1033 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.6996 (m-10) REVERT: B 1133 MET cc_start: 0.5216 (tmt) cc_final: 0.4874 (mpp) REVERT: B 1186 ASP cc_start: 0.7511 (p0) cc_final: 0.7164 (p0) REVERT: B 1194 ILE cc_start: 0.8646 (pp) cc_final: 0.8411 (pp) REVERT: C 100 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.8168 (mmm-85) REVERT: C 216 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7610 (t-90) REVERT: D 23 HIS cc_start: 0.5105 (OUTLIER) cc_final: 0.4511 (m170) REVERT: D 38 GLN cc_start: 0.6142 (tp-100) cc_final: 0.5040 (mp10) REVERT: E 135 PHE cc_start: 0.7449 (m-80) cc_final: 0.6928 (m-10) REVERT: E 137 GLU cc_start: 0.7213 (pt0) cc_final: 0.6853 (pt0) REVERT: E 143 ASN cc_start: 0.8383 (t0) cc_final: 0.8131 (t0) REVERT: E 179 GLN cc_start: 0.8566 (tp40) cc_final: 0.8195 (mt0) REVERT: E 182 ASP cc_start: 0.7840 (t70) cc_final: 0.7623 (t70) REVERT: G 59 GLN cc_start: 0.7777 (tt0) cc_final: 0.6801 (mp10) REVERT: G 90 LEU cc_start: 0.7997 (mp) cc_final: 0.7212 (mp) REVERT: G 119 HIS cc_start: 0.6158 (m-70) cc_final: 0.5843 (m-70) REVERT: J 49 MET cc_start: 0.8403 (mmt) cc_final: 0.8188 (mmm) REVERT: J 64 ASN cc_start: 0.8132 (t0) cc_final: 0.7659 (t0) REVERT: J 69 ARG cc_start: 0.6408 (mmp-170) cc_final: 0.6136 (mmp-170) REVERT: K 67 GLU cc_start: 0.6516 (pp20) cc_final: 0.5548 (pp20) REVERT: K 68 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8189 (mm-30) REVERT: K 69 ASP cc_start: 0.8461 (t0) cc_final: 0.8100 (t0) REVERT: K 114 VAL cc_start: 0.7795 (p) cc_final: 0.7552 (t) REVERT: K 125 MET cc_start: 0.7173 (mmm) cc_final: 0.6769 (tpp) REVERT: K 128 CYS cc_start: 0.7339 (p) cc_final: 0.7055 (p) REVERT: L 40 LEU cc_start: 0.5441 (OUTLIER) cc_final: 0.4989 (pp) REVERT: L 49 LYS cc_start: 0.5858 (mppt) cc_final: 0.5550 (ttmt) REVERT: N 40 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5449 (pp) REVERT: N 107 MET cc_start: 0.5918 (OUTLIER) cc_final: 0.4466 (mpp) outliers start: 199 outliers final: 121 residues processed: 723 average time/residue: 0.2106 time to fit residues: 254.2170 Evaluate side-chains 659 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 522 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL 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 98 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 399 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 621 THR 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 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 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 1123 VAL Chi-restraints excluded: chain A residue 1179 ILE 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 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 195 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 261 ARG 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 465 LEU Chi-restraints excluded: chain B residue 476 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 695 ASN 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 787 MET 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 913 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 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 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 127 THR Chi-restraints excluded: chain C residue 216 HIS 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 29 PHE 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 156 LEU 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 125 LEU Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 62 MET 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 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 48 VAL 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 97 SER Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 40 LEU 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 40 LEU 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: 0.6980 chunk 373 optimal weight: 4.9990 chunk 394 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 368 optimal weight: 3.9990 chunk 316 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** 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** A1592 GLN B 243 GLN ** 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 ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 HIS ** E 54 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.167322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141719 restraints weight = 70278.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.144236 restraints weight = 42726.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144885 restraints weight = 29942.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.145797 restraints weight = 25483.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.145910 restraints weight = 22252.257| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 34887 Z= 0.192 Angle : 0.756 18.036 47340 Z= 0.374 Chirality : 0.047 0.226 5292 Planarity : 0.005 0.060 5936 Dihedral : 11.717 85.145 5113 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.77 % Favored : 91.16 % Rotamer: Outliers : 5.58 % Allowed : 21.88 % Favored : 72.54 % 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 aren not related in a simple way. whole: -2.40 (0.13), residues: 4093 helix: -0.81 (0.14), residues: 1266 sheet: -1.60 (0.21), residues: 555 loop : -2.08 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 162 TYR 0.037 0.002 TYR B 641 PHE 0.036 0.002 PHE A1535 TRP 0.015 0.002 TRP B 836 HIS 0.009 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00445 (34863) covalent geometry : angle 0.74212 (47313) hydrogen bonds : bond 0.04203 ( 1105) hydrogen bonds : angle 5.80904 ( 3058) metal coordination : bond 0.01115 ( 23) metal coordination : angle 6.18349 ( 27) Misc. bond : bond 0.00221 ( 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 745 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 539 time to evaluate : 1.313 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: 0.6580 (t0) cc_final: 0.5831 (m-30) REVERT: A 24 ILE cc_start: 0.7911 (pt) cc_final: 0.7573 (tp) REVERT: A 221 HIS cc_start: 0.7217 (t-90) cc_final: 0.7015 (t-90) REVERT: A 464 GLU cc_start: 0.5719 (tm-30) cc_final: 0.5370 (tm-30) REVERT: A 471 MET cc_start: 0.8506 (mmm) cc_final: 0.7735 (mpp) REVERT: A 601 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8162 (ttp) REVERT: A 610 ASN cc_start: 0.7296 (t0) cc_final: 0.6090 (t0) REVERT: A 756 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6433 (tmtt) REVERT: A 772 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7475 (tppt) REVERT: A 937 ASN cc_start: 0.7062 (t0) cc_final: 0.6793 (t0) REVERT: A 977 MET cc_start: 0.7676 (ttt) cc_final: 0.7349 (ttt) REVERT: A 997 PHE cc_start: 0.7280 (m-80) cc_final: 0.6883 (m-80) REVERT: A 1000 MET cc_start: 0.7520 (mtm) cc_final: 0.7273 (mtm) REVERT: A 1146 SER cc_start: 0.9010 (m) cc_final: 0.8249 (t) REVERT: A 1223 ARG cc_start: 0.8104 (tmm160) cc_final: 0.7693 (tmt170) REVERT: A 1227 MET cc_start: 0.8050 (mpt) cc_final: 0.7717 (mpt) REVERT: A 1439 MET cc_start: 0.1576 (tmm) cc_final: 0.1324 (tmm) REVERT: A 1485 MET cc_start: 0.5250 (mmm) cc_final: 0.5049 (mmm) REVERT: A 1575 ILE cc_start: 0.8216 (pp) cc_final: 0.7908 (tp) REVERT: A 1603 MET cc_start: 0.7486 (ptp) cc_final: 0.7237 (ptp) REVERT: A 1611 MET cc_start: 0.7446 (mmm) cc_final: 0.6974 (tpp) REVERT: A 1615 TYR cc_start: 0.8384 (t80) cc_final: 0.8175 (t80) REVERT: B 46 ILE cc_start: 0.7987 (mm) cc_final: 0.7181 (pt) REVERT: B 205 MET cc_start: 0.8077 (mtp) cc_final: 0.7769 (mtp) REVERT: B 261 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7550 (ttp-170) REVERT: B 473 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7765 (tm-30) REVERT: B 481 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8792 (p) REVERT: B 566 TYR cc_start: 0.7092 (t80) cc_final: 0.6773 (t80) REVERT: B 672 MET cc_start: 0.7790 (ppp) cc_final: 0.6959 (ppp) REVERT: B 764 ASN cc_start: 0.7237 (m-40) cc_final: 0.6986 (m-40) REVERT: B 841 ASP cc_start: 0.6363 (m-30) cc_final: 0.6073 (p0) REVERT: B 935 ASP cc_start: 0.7284 (t0) cc_final: 0.6852 (t70) REVERT: B 946 ASP cc_start: 0.8033 (m-30) cc_final: 0.7539 (m-30) REVERT: B 1007 TYR cc_start: 0.8434 (t80) cc_final: 0.7843 (t80) REVERT: B 1013 MET cc_start: 0.7854 (mtp) cc_final: 0.7533 (mtt) REVERT: B 1033 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7199 (m-10) REVERT: B 1080 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7683 (tp) REVERT: B 1133 MET cc_start: 0.5327 (OUTLIER) cc_final: 0.4967 (mpp) REVERT: B 1186 ASP cc_start: 0.7608 (p0) cc_final: 0.7225 (p0) REVERT: C 216 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7328 (t-170) REVERT: D 23 HIS cc_start: 0.5203 (OUTLIER) cc_final: 0.4384 (m-70) REVERT: D 38 GLN cc_start: 0.6230 (tp-100) cc_final: 0.5080 (mp10) REVERT: E 135 PHE cc_start: 0.7416 (m-80) cc_final: 0.7033 (m-10) REVERT: E 137 GLU cc_start: 0.7241 (pt0) cc_final: 0.6961 (pt0) REVERT: E 179 GLN cc_start: 0.8621 (tp40) cc_final: 0.8289 (mt0) REVERT: G 59 GLN cc_start: 0.7913 (tt0) cc_final: 0.6836 (mp10) REVERT: G 90 LEU cc_start: 0.8130 (mp) cc_final: 0.7615 (mp) REVERT: H 146 ARG cc_start: 0.4528 (OUTLIER) cc_final: 0.4165 (pmt-80) REVERT: J 49 MET cc_start: 0.8525 (mmt) cc_final: 0.8324 (mmm) REVERT: J 64 ASN cc_start: 0.8249 (t0) cc_final: 0.7802 (t0) REVERT: K 67 GLU cc_start: 0.6607 (pp20) cc_final: 0.5559 (pp20) REVERT: K 68 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7987 (mm-30) REVERT: K 69 ASP cc_start: 0.8646 (t0) cc_final: 0.8350 (t0) REVERT: K 114 VAL cc_start: 0.7813 (p) cc_final: 0.7570 (t) REVERT: K 122 LYS cc_start: 0.8231 (tppt) cc_final: 0.7944 (ttpp) REVERT: K 125 MET cc_start: 0.7156 (mmm) cc_final: 0.6644 (tpp) REVERT: L 49 LYS cc_start: 0.5664 (mppt) cc_final: 0.5352 (ttmt) REVERT: M 52 VAL cc_start: 0.6447 (OUTLIER) cc_final: 0.6246 (t) REVERT: N 40 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5518 (pp) REVERT: N 107 MET cc_start: 0.5856 (OUTLIER) cc_final: 0.4521 (mpp) outliers start: 206 outliers final: 138 residues processed: 688 average time/residue: 0.2195 time to fit residues: 249.8142 Evaluate side-chains 653 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 501 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 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 514 TYR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 621 THR 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 816 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 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 962 SER 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 1179 ILE 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 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 261 ARG 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 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 531 VAL Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 667 PHE 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 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 1028 VAL 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 1109 SER Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1133 MET 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 127 THR Chi-restraints excluded: chain C residue 216 HIS 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 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 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 108 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 62 MET 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 42 PHE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 52 THR 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 97 SER Chi-restraints excluded: chain K residue 107 THR 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 40 LEU 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 40 LEU 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: 2.9990 chunk 212 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 245 optimal weight: 9.9990 chunk 336 optimal weight: 9.9990 chunk 398 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 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 547 HIS B 587 GLN ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** 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 = 0.4105 r_free = 0.4105 target = 0.162981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136730 restraints weight = 70870.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.139094 restraints weight = 42643.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140676 restraints weight = 30268.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141637 restraints weight = 24178.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142338 restraints weight = 21068.450| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 34887 Z= 0.250 Angle : 0.823 19.551 47340 Z= 0.411 Chirality : 0.049 0.266 5292 Planarity : 0.006 0.062 5936 Dihedral : 11.907 85.181 5113 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.87 % Favored : 90.06 % Rotamer: Outliers : 5.88 % Allowed : 22.23 % Favored : 71.89 % 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 aren not related in a simple way. whole: -2.50 (0.13), residues: 4093 helix: -0.90 (0.14), residues: 1255 sheet: -1.75 (0.21), residues: 557 loop : -2.13 (0.13), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 162 TYR 0.034 0.003 TYR A 697 PHE 0.029 0.002 PHE A1535 TRP 0.021 0.002 TRP B 611 HIS 0.018 0.002 HIS D 23 Details of bonding type rmsd covalent geometry : bond 0.00574 (34863) covalent geometry : angle 0.80634 (47313) hydrogen bonds : bond 0.04590 ( 1105) hydrogen bonds : angle 6.03008 ( 3058) metal coordination : bond 0.01314 ( 23) metal coordination : angle 6.97841 ( 27) Misc. bond : bond 0.00221 ( 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 744 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 527 time to evaluate : 1.411 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: 0.6828 (t0) cc_final: 0.6085 (m-30) REVERT: A 221 HIS cc_start: 0.7556 (t-90) cc_final: 0.7325 (t-90) REVERT: A 464 GLU cc_start: 0.6187 (tm-30) cc_final: 0.5767 (tm-30) REVERT: A 471 MET cc_start: 0.8531 (mmm) cc_final: 0.7687 (mpp) REVERT: A 601 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8164 (ttp) REVERT: A 744 MET cc_start: 0.7893 (mmm) cc_final: 0.7646 (mmt) REVERT: A 756 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6875 (tmtt) REVERT: A 772 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7937 (tptt) REVERT: A 977 MET cc_start: 0.7927 (ttt) cc_final: 0.7482 (ttt) REVERT: A 997 PHE cc_start: 0.7385 (m-80) cc_final: 0.7014 (m-80) REVERT: A 1000 MET cc_start: 0.7582 (mtm) cc_final: 0.7352 (mtm) REVERT: A 1146 SER cc_start: 0.8945 (m) cc_final: 0.8214 (t) REVERT: A 1223 ARG cc_start: 0.8246 (tmm160) cc_final: 0.7917 (tmt170) REVERT: A 1227 MET cc_start: 0.8179 (mpt) cc_final: 0.7968 (mpt) REVERT: A 1485 MET cc_start: 0.5879 (mmm) cc_final: 0.5626 (mmm) REVERT: A 1575 ILE cc_start: 0.8222 (pp) cc_final: 0.7935 (tp) REVERT: A 1603 MET cc_start: 0.7680 (ptp) cc_final: 0.7419 (ptp) REVERT: A 1611 MET cc_start: 0.7504 (mmm) cc_final: 0.7066 (tpp) REVERT: B 217 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6183 (mt) REVERT: B 261 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7686 (ttp-170) REVERT: B 480 GLN cc_start: 0.7758 (pt0) cc_final: 0.7455 (pt0) REVERT: B 481 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8851 (p) REVERT: B 566 TYR cc_start: 0.7362 (t80) cc_final: 0.6900 (t80) REVERT: B 641 TYR cc_start: 0.7305 (m-80) cc_final: 0.6310 (m-80) REVERT: B 672 MET cc_start: 0.7912 (ppp) cc_final: 0.7012 (ppp) REVERT: B 764 ASN cc_start: 0.7287 (m-40) cc_final: 0.7011 (m-40) REVERT: B 841 ASP cc_start: 0.6987 (m-30) cc_final: 0.6458 (p0) REVERT: B 935 ASP cc_start: 0.7404 (t0) cc_final: 0.7016 (t70) REVERT: B 946 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: B 950 ASN cc_start: 0.7342 (OUTLIER) cc_final: 0.7111 (m-40) REVERT: B 1007 TYR cc_start: 0.8542 (t80) cc_final: 0.7905 (t80) REVERT: B 1013 MET cc_start: 0.7937 (mtp) cc_final: 0.7585 (mtt) REVERT: B 1033 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7414 (m-10) REVERT: B 1080 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7796 (tp) REVERT: B 1133 MET cc_start: 0.5304 (OUTLIER) cc_final: 0.4905 (mpp) REVERT: C 216 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7143 (t-170) REVERT: D 37 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.5167 (pp) REVERT: D 38 GLN cc_start: 0.6584 (tp-100) cc_final: 0.5273 (mp10) REVERT: E 137 GLU cc_start: 0.7606 (pt0) cc_final: 0.7376 (pt0) REVERT: E 179 GLN cc_start: 0.8651 (tp40) cc_final: 0.8201 (mt0) REVERT: G 22 LYS cc_start: 0.4054 (OUTLIER) cc_final: 0.2682 (tptt) REVERT: G 59 GLN cc_start: 0.7938 (tt0) cc_final: 0.6626 (mp10) REVERT: G 90 LEU cc_start: 0.8234 (mp) cc_final: 0.7895 (mp) REVERT: G 217 TRP cc_start: 0.5877 (p90) cc_final: 0.5593 (p90) REVERT: H 146 ARG cc_start: 0.4623 (OUTLIER) cc_final: 0.4287 (pmt-80) REVERT: J 1 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.4692 (tmt) REVERT: J 64 ASN cc_start: 0.8613 (t0) cc_final: 0.8044 (t0) REVERT: K 69 ASP cc_start: 0.8742 (t0) cc_final: 0.8476 (t0) REVERT: K 114 VAL cc_start: 0.7692 (p) cc_final: 0.7464 (t) REVERT: K 122 LYS cc_start: 0.8024 (tppt) cc_final: 0.7786 (ttpp) REVERT: L 40 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.5177 (pp) REVERT: L 49 LYS cc_start: 0.5691 (mppt) cc_final: 0.5422 (ttmt) REVERT: N 40 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5523 (pp) REVERT: N 107 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.4798 (mpp) REVERT: N 175 TYR cc_start: 0.2306 (OUTLIER) cc_final: 0.1609 (p90) outliers start: 217 outliers final: 149 residues processed: 692 average time/residue: 0.2182 time to fit residues: 252.4927 Evaluate side-chains 655 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 486 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 178 LEU 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 399 LEU 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 571 HIS Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 621 THR 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 780 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 816 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 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 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 A residue 1662 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 119 ARG 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 217 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 303 THR 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 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 531 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 719 CYS Chi-restraints excluded: chain B residue 721 MET 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 852 VAL Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1015 SER Chi-restraints excluded: chain B residue 1028 VAL 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 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 1133 MET 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 111 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 216 HIS 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 54 GLN Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 141 VAL 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 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 F residue 137 TYR Chi-restraints excluded: chain F residue 145 ASP 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 62 MET 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 42 PHE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 60 PHE 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 40 LEU 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 40 LEU Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 40 LEU 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 160 VAL Chi-restraints excluded: chain N residue 175 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 100 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 321 optimal weight: 0.0060 chunk 117 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 384 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN 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** B 547 HIS B 646 HIS ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 695 ASN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 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 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** K 70 HIS M 75 GLN ** 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 = 0.4156 r_free = 0.4156 target = 0.167379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141184 restraints weight = 69871.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.143831 restraints weight = 40501.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.145581 restraints weight = 27873.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146663 restraints weight = 21832.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.147215 restraints weight = 18732.230| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34887 Z= 0.147 Angle : 0.764 17.073 47340 Z= 0.374 Chirality : 0.047 0.405 5292 Planarity : 0.005 0.060 5936 Dihedral : 11.760 82.664 5112 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.18 % Favored : 91.74 % Rotamer: Outliers : 4.66 % Allowed : 24.07 % Favored : 71.27 % 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 aren not related in a simple way. whole: -2.30 (0.13), residues: 4093 helix: -0.71 (0.14), residues: 1256 sheet: -1.62 (0.22), residues: 550 loop : -2.02 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 55 TYR 0.038 0.002 TYR G 84 PHE 0.024 0.002 PHE E 96 TRP 0.019 0.001 TRP B 984 HIS 0.011 0.001 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00337 (34863) covalent geometry : angle 0.75197 (47313) hydrogen bonds : bond 0.04035 ( 1105) hydrogen bonds : angle 5.77164 ( 3058) metal coordination : bond 0.01347 ( 23) metal coordination : angle 5.75086 ( 27) Misc. bond : bond 0.00222 ( 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 728 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 556 time to evaluate : 1.328 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: 0.6665 (t0) cc_final: 0.5962 (m-30) REVERT: A 221 HIS cc_start: 0.7463 (t-90) cc_final: 0.7197 (t-90) REVERT: A 368 ARG cc_start: 0.8370 (mtm110) cc_final: 0.8006 (mtm110) REVERT: A 464 GLU cc_start: 0.5666 (tm-30) cc_final: 0.5217 (tm-30) REVERT: A 471 MET cc_start: 0.8402 (mmm) cc_final: 0.7604 (mpp) REVERT: A 635 MET cc_start: 0.7383 (ttt) cc_final: 0.7072 (ttt) REVERT: A 744 MET cc_start: 0.7897 (mmm) cc_final: 0.7656 (mmt) REVERT: A 756 LYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6434 (tmtt) REVERT: A 772 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7839 (tptt) REVERT: A 843 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7216 (ttt90) REVERT: A 977 MET cc_start: 0.7785 (ttt) cc_final: 0.7360 (ttt) REVERT: A 997 PHE cc_start: 0.7285 (m-80) cc_final: 0.6950 (m-80) REVERT: A 1000 MET cc_start: 0.7398 (mtm) cc_final: 0.6949 (mtm) REVERT: A 1146 SER cc_start: 0.9099 (m) cc_final: 0.8184 (t) REVERT: A 1150 LYS cc_start: 0.7989 (mptt) cc_final: 0.7702 (mtpp) REVERT: A 1183 GLU cc_start: 0.6878 (tp30) cc_final: 0.6653 (tp30) REVERT: A 1223 ARG cc_start: 0.8171 (tmm160) cc_final: 0.7730 (tmt170) REVERT: A 1227 MET cc_start: 0.8114 (mpt) cc_final: 0.6580 (mmt) REVERT: A 1485 MET cc_start: 0.5832 (mmm) cc_final: 0.5610 (mmm) REVERT: A 1613 MET cc_start: 0.7533 (mmt) cc_final: 0.7183 (mmt) REVERT: B 260 PHE cc_start: 0.6572 (t80) cc_final: 0.6255 (t80) REVERT: B 411 MET cc_start: 0.8183 (mmm) cc_final: 0.7935 (mmp) REVERT: B 461 MET cc_start: 0.8350 (mmp) cc_final: 0.7862 (mmp) REVERT: B 481 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8810 (p) REVERT: B 566 TYR cc_start: 0.7374 (t80) cc_final: 0.6892 (t80) REVERT: B 641 TYR cc_start: 0.7178 (m-80) cc_final: 0.6815 (m-80) REVERT: B 672 MET cc_start: 0.7842 (ppp) cc_final: 0.6797 (ppp) REVERT: B 717 TYR cc_start: 0.7110 (t80) cc_final: 0.6905 (t80) REVERT: B 764 ASN cc_start: 0.7293 (m-40) cc_final: 0.7054 (m-40) REVERT: B 841 ASP cc_start: 0.6932 (m-30) cc_final: 0.6440 (p0) REVERT: B 924 LYS cc_start: 0.7572 (mttp) cc_final: 0.7291 (mmtp) REVERT: B 950 ASN cc_start: 0.7158 (OUTLIER) cc_final: 0.6925 (m-40) REVERT: B 1007 TYR cc_start: 0.8514 (t80) cc_final: 0.7827 (t80) REVERT: B 1033 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: B 1180 PHE cc_start: 0.8566 (t80) cc_final: 0.8242 (t80) REVERT: C 216 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7151 (t-170) REVERT: D 37 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.5094 (pp) REVERT: D 38 GLN cc_start: 0.6572 (tp-100) cc_final: 0.5288 (mp10) REVERT: E 137 GLU cc_start: 0.7293 (pt0) cc_final: 0.6968 (pt0) REVERT: E 143 ASN cc_start: 0.8639 (t0) cc_final: 0.8341 (t0) REVERT: E 179 GLN cc_start: 0.8541 (tp40) cc_final: 0.8229 (mt0) REVERT: F 57 ASP cc_start: 0.8202 (p0) cc_final: 0.7771 (p0) REVERT: F 61 HIS cc_start: 0.6759 (m-70) cc_final: 0.6548 (m90) REVERT: F 100 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7654 (tm-30) REVERT: G 22 LYS cc_start: 0.4154 (OUTLIER) cc_final: 0.2787 (tptt) REVERT: G 59 GLN cc_start: 0.7803 (tt0) cc_final: 0.6736 (mp10) REVERT: G 217 TRP cc_start: 0.5918 (p90) cc_final: 0.5627 (p90) REVERT: H 146 ARG cc_start: 0.4394 (OUTLIER) cc_final: 0.4163 (pmt-80) REVERT: J 1 MET cc_start: 0.5383 (OUTLIER) cc_final: 0.4034 (tmt) REVERT: J 49 MET cc_start: 0.9155 (mmm) cc_final: 0.8756 (mmt) REVERT: J 64 ASN cc_start: 0.8704 (t0) cc_final: 0.8128 (t0) REVERT: K 67 GLU cc_start: 0.6754 (pp20) cc_final: 0.6287 (pp20) REVERT: K 69 ASP cc_start: 0.8655 (t0) cc_final: 0.8453 (t0) REVERT: K 81 MET cc_start: 0.7326 (ttm) cc_final: 0.7116 (ptp) REVERT: K 104 ARG cc_start: 0.6073 (tpt-90) cc_final: 0.5784 (tpt-90) REVERT: K 122 LYS cc_start: 0.8232 (tppt) cc_final: 0.7878 (ttpp) REVERT: L 40 LEU cc_start: 0.5289 (OUTLIER) cc_final: 0.5071 (pp) REVERT: L 57 LEU cc_start: 0.8105 (mm) cc_final: 0.7845 (mp) REVERT: M 75 GLN cc_start: 0.4486 (tt0) cc_final: 0.4226 (tt0) REVERT: N 40 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5516 (pp) REVERT: N 107 MET cc_start: 0.6056 (OUTLIER) cc_final: 0.4946 (mpp) REVERT: N 175 TYR cc_start: 0.2250 (OUTLIER) cc_final: 0.1792 (p90) outliers start: 172 outliers final: 124 residues processed: 683 average time/residue: 0.1824 time to fit residues: 206.8161 Evaluate side-chains 650 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 511 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 399 LEU 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 621 THR 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 780 ILE Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 843 ARG 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 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 916 THR 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 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 1616 GLU Chi-restraints excluded: chain A residue 1617 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 A residue 1662 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 MET 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 292 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 359 LEU 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 433 ASN 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 531 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 719 CYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 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 950 ASN Chi-restraints excluded: chain B residue 1015 SER Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain B residue 1189 LEU 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 127 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 216 HIS 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 165 LEU 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 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 62 MET 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 42 PHE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 60 PHE 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 40 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 175 TYR 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: 6.9990 chunk 150 optimal weight: 0.7980 chunk 307 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 345 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 356 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** 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** B 547 HIS B 646 HIS ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** 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 56 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** L 66 GLN ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.163834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137880 restraints weight = 70125.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140601 restraints weight = 43185.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141179 restraints weight = 29486.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.142024 restraints weight = 26986.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.143445 restraints weight = 22131.878| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.5425 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= 0.210 Angle : 0.810 20.924 47340 Z= 0.402 Chirality : 0.048 0.377 5292 Planarity : 0.005 0.059 5936 Dihedral : 11.867 84.918 5111 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.07 % Favored : 89.86 % Rotamer: Outliers : 5.01 % Allowed : 23.99 % Favored : 70.99 % 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 aren not related in a simple way. whole: -2.33 (0.13), residues: 4093 helix: -0.77 (0.14), residues: 1244 sheet: -1.60 (0.22), residues: 533 loop : -2.02 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1015 TYR 0.033 0.002 TYR G 84 PHE 0.028 0.002 PHE B 643 TRP 0.021 0.002 TRP B 931 HIS 0.010 0.002 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00488 (34863) covalent geometry : angle 0.79787 (47313) hydrogen bonds : bond 0.04296 ( 1105) hydrogen bonds : angle 5.88818 ( 3058) metal coordination : bond 0.01337 ( 23) metal coordination : angle 5.78707 ( 27) Misc. bond : bond 0.00218 ( 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 709 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 524 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.6884 (t0) cc_final: 0.6166 (m-30) REVERT: A 464 GLU cc_start: 0.6090 (tm-30) cc_final: 0.5728 (tm-30) REVERT: A 604 LYS cc_start: 0.7972 (mmmt) cc_final: 0.7517 (tptp) REVERT: A 744 MET cc_start: 0.7880 (mmm) cc_final: 0.7618 (mmt) REVERT: A 772 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7871 (tptt) REVERT: A 843 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6787 (mtp85) REVERT: A 977 MET cc_start: 0.7841 (ttt) cc_final: 0.7399 (ttt) REVERT: A 997 PHE cc_start: 0.7360 (m-80) cc_final: 0.6958 (m-80) REVERT: A 1000 MET cc_start: 0.7540 (mtm) cc_final: 0.7095 (mtm) REVERT: A 1146 SER cc_start: 0.9060 (m) cc_final: 0.8192 (t) REVERT: A 1150 LYS cc_start: 0.8090 (mptt) cc_final: 0.7860 (mtpp) REVERT: A 1223 ARG cc_start: 0.8279 (tmm160) cc_final: 0.7878 (tmt170) REVERT: A 1227 MET cc_start: 0.8009 (mpt) cc_final: 0.7795 (mpt) REVERT: A 1611 MET cc_start: 0.7782 (mmm) cc_final: 0.6600 (mmm) REVERT: A 1634 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7922 (pp) REVERT: B 411 MET cc_start: 0.8169 (mmm) cc_final: 0.7943 (mmp) REVERT: B 481 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8836 (p) REVERT: B 512 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6198 (tt) REVERT: B 566 TYR cc_start: 0.7262 (t80) cc_final: 0.6157 (t80) REVERT: B 641 TYR cc_start: 0.7371 (m-80) cc_final: 0.7064 (m-80) REVERT: B 672 MET cc_start: 0.7983 (ppp) cc_final: 0.6964 (ppp) REVERT: B 764 ASN cc_start: 0.7234 (m-40) cc_final: 0.6988 (m-40) REVERT: B 841 ASP cc_start: 0.7059 (m-30) cc_final: 0.6458 (p0) REVERT: B 939 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8471 (p) REVERT: B 950 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.7165 (m-40) REVERT: B 1007 TYR cc_start: 0.8523 (t80) cc_final: 0.7722 (t80) REVERT: B 1033 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7356 (m-10) REVERT: B 1080 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7717 (tp) REVERT: B 1180 PHE cc_start: 0.8621 (t80) cc_final: 0.8400 (t80) REVERT: C 216 HIS cc_start: 0.8330 (OUTLIER) cc_final: 0.7280 (t-170) REVERT: D 37 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.5065 (pp) REVERT: D 38 GLN cc_start: 0.6200 (tp-100) cc_final: 0.5152 (mp10) REVERT: E 137 GLU cc_start: 0.7591 (pt0) cc_final: 0.7365 (pt0) REVERT: E 143 ASN cc_start: 0.8795 (t0) cc_final: 0.8503 (t0) REVERT: F 61 HIS cc_start: 0.6756 (m-70) cc_final: 0.6438 (m90) REVERT: F 100 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7680 (tm-30) REVERT: G 22 LYS cc_start: 0.3884 (OUTLIER) cc_final: 0.2466 (tptt) REVERT: G 59 GLN cc_start: 0.7443 (tt0) cc_final: 0.6364 (mm-40) REVERT: G 217 TRP cc_start: 0.6232 (p90) cc_final: 0.5953 (p90) REVERT: H 146 ARG cc_start: 0.4488 (OUTLIER) cc_final: 0.4247 (pmt-80) REVERT: J 1 MET cc_start: 0.5731 (OUTLIER) cc_final: 0.4743 (tmt) REVERT: J 64 ASN cc_start: 0.8595 (t0) cc_final: 0.8029 (t0) REVERT: K 67 GLU cc_start: 0.7067 (pp20) cc_final: 0.6695 (pp20) REVERT: K 68 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8555 (mm-30) REVERT: L 57 LEU cc_start: 0.8072 (mm) cc_final: 0.7801 (mp) REVERT: N 40 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5504 (pp) REVERT: N 107 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.5032 (mpp) REVERT: N 175 TYR cc_start: 0.2336 (OUTLIER) cc_final: 0.1838 (p90) outliers start: 185 outliers final: 138 residues processed: 662 average time/residue: 0.1763 time to fit residues: 194.3687 Evaluate side-chains 653 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 498 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 399 LEU 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 571 HIS 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 769 VAL Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 843 ARG 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 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 1123 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1246 VAL 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 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 1634 LEU 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 102 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 MET 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 292 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 359 LEU 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 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 667 PHE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 719 CYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 787 MET 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 939 SER Chi-restraints excluded: chain B residue 950 ASN 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 1126 VAL Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain B residue 1189 LEU 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 127 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 216 HIS 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 141 VAL 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 108 PHE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain F residue 145 ASP 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 62 MET 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 42 PHE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 128 CYS Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 111 VAL 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: 9.9990 chunk 375 optimal weight: 20.0000 chunk 254 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 361 optimal weight: 9.9990 chunk 402 optimal weight: 3.9990 chunk 352 optimal weight: 7.9990 chunk 365 optimal weight: 0.5980 chunk 201 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** 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 547 HIS B 646 HIS ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 695 ASN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 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 ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** 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 = 0.4132 r_free = 0.4132 target = 0.165448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139424 restraints weight = 70557.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141885 restraints weight = 41696.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.143496 restraints weight = 29146.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.144618 restraints weight = 23033.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.145269 restraints weight = 19867.177| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34887 Z= 0.170 Angle : 0.798 15.392 47340 Z= 0.394 Chirality : 0.047 0.324 5292 Planarity : 0.005 0.062 5936 Dihedral : 11.825 84.406 5111 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.75 % Favored : 91.18 % Rotamer: Outliers : 4.53 % Allowed : 24.61 % Favored : 70.86 % 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 aren not related in a simple way. whole: -2.23 (0.13), residues: 4093 helix: -0.69 (0.14), residues: 1248 sheet: -1.49 (0.23), residues: 524 loop : -1.97 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 648 TYR 0.030 0.002 TYR G 84 PHE 0.025 0.002 PHE A 420 TRP 0.017 0.002 TRP B 611 HIS 0.009 0.001 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00396 (34863) covalent geometry : angle 0.78768 (47313) hydrogen bonds : bond 0.04087 ( 1105) hydrogen bonds : angle 5.78240 ( 3058) metal coordination : bond 0.01370 ( 23) metal coordination : angle 5.50213 ( 27) Misc. bond : bond 0.00217 ( 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 696 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 529 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.6789 (t0) cc_final: 0.6097 (m-30) REVERT: A 368 ARG cc_start: 0.8393 (mtm110) cc_final: 0.7912 (mtm110) REVERT: A 464 GLU cc_start: 0.5941 (tm-30) cc_final: 0.5634 (tm-30) REVERT: A 604 LYS cc_start: 0.7956 (mmmt) cc_final: 0.7550 (tptp) REVERT: A 744 MET cc_start: 0.7895 (mmm) cc_final: 0.7678 (mmt) REVERT: A 756 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6619 (tmtt) REVERT: A 772 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7739 (tptt) REVERT: A 785 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7864 (tp-100) REVERT: A 833 LEU cc_start: 0.8073 (tp) cc_final: 0.7784 (tt) REVERT: A 843 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6904 (mtp85) REVERT: A 977 MET cc_start: 0.7878 (ttt) cc_final: 0.7392 (ttt) REVERT: A 997 PHE cc_start: 0.7322 (m-80) cc_final: 0.6908 (m-80) REVERT: A 1000 MET cc_start: 0.7517 (mtm) cc_final: 0.7064 (mtm) REVERT: A 1146 SER cc_start: 0.9081 (m) cc_final: 0.8194 (t) REVERT: A 1223 ARG cc_start: 0.8229 (tmm160) cc_final: 0.7817 (tmt170) REVERT: A 1611 MET cc_start: 0.7783 (mmm) cc_final: 0.6611 (mmm) REVERT: A 1634 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7800 (pp) REVERT: B 411 MET cc_start: 0.8227 (mmm) cc_final: 0.7995 (mmp) REVERT: B 473 GLN cc_start: 0.8803 (tt0) cc_final: 0.8162 (tm-30) REVERT: B 481 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8786 (p) REVERT: B 641 TYR cc_start: 0.7503 (m-80) cc_final: 0.7192 (m-80) REVERT: B 668 GLU cc_start: 0.6634 (tm-30) cc_final: 0.6335 (tm-30) REVERT: B 672 MET cc_start: 0.7892 (ppp) cc_final: 0.6927 (ppp) REVERT: B 764 ASN cc_start: 0.7238 (m-40) cc_final: 0.6964 (m-40) REVERT: B 841 ASP cc_start: 0.7015 (m-30) cc_final: 0.6457 (p0) REVERT: B 939 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8580 (p) REVERT: B 950 ASN cc_start: 0.7155 (OUTLIER) cc_final: 0.6860 (m-40) REVERT: B 1007 TYR cc_start: 0.8510 (t80) cc_final: 0.7849 (t80) REVERT: B 1033 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7303 (m-10) REVERT: B 1180 PHE cc_start: 0.8583 (t80) cc_final: 0.8328 (t80) REVERT: C 155 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5537 (mt-10) REVERT: C 216 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.7232 (t-170) REVERT: D 37 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.4990 (pp) REVERT: D 38 GLN cc_start: 0.6244 (tp-100) cc_final: 0.5178 (mp10) REVERT: E 137 GLU cc_start: 0.7478 (pt0) cc_final: 0.7242 (pt0) REVERT: E 143 ASN cc_start: 0.8774 (t0) cc_final: 0.8472 (t0) REVERT: F 61 HIS cc_start: 0.6768 (m-70) cc_final: 0.6474 (m90) REVERT: F 100 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7661 (tm-30) REVERT: G 22 LYS cc_start: 0.3902 (OUTLIER) cc_final: 0.2443 (tptt) REVERT: G 59 GLN cc_start: 0.7576 (tt0) cc_final: 0.6344 (mm-40) REVERT: G 217 TRP cc_start: 0.5967 (p90) cc_final: 0.5677 (p90) REVERT: H 115 TYR cc_start: 0.6048 (m-80) cc_final: 0.5830 (m-80) REVERT: H 146 ARG cc_start: 0.4358 (OUTLIER) cc_final: 0.4150 (pmt-80) REVERT: J 49 MET cc_start: 0.9128 (mmm) cc_final: 0.8818 (mmt) REVERT: J 64 ASN cc_start: 0.8618 (t0) cc_final: 0.8137 (t0) REVERT: K 67 GLU cc_start: 0.7258 (pp20) cc_final: 0.6823 (pp20) REVERT: K 68 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8618 (mm-30) REVERT: K 122 LYS cc_start: 0.8193 (tppt) cc_final: 0.7793 (ttpp) REVERT: L 57 LEU cc_start: 0.8165 (mm) cc_final: 0.7942 (mp) REVERT: N 40 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5482 (pp) REVERT: N 107 MET cc_start: 0.6127 (OUTLIER) cc_final: 0.4995 (mpp) REVERT: N 175 TYR cc_start: 0.2319 (OUTLIER) cc_final: 0.1852 (p90) outliers start: 167 outliers final: 134 residues processed: 648 average time/residue: 0.1853 time to fit residues: 199.8080 Evaluate side-chains 662 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 512 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL 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 178 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 399 LEU 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 571 HIS 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 769 VAL Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 843 ARG 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 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 1123 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1246 VAL 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 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 1634 LEU 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 102 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 MET 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 253 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 359 LEU 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 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 531 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 787 MET 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 939 SER Chi-restraints excluded: chain B residue 950 ASN 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 1126 VAL Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain B residue 1189 LEU 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 127 THR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 216 HIS 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 141 VAL 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 108 PHE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain F residue 145 ASP 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 56 ASN Chi-restraints excluded: chain G residue 62 MET 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 H residue 146 ARG 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 39 LEU Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 128 CYS Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 111 VAL 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: 9.9990 chunk 179 optimal weight: 0.9990 chunk 287 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 252 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 380 ASN ** 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 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** 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** ** A1662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 646 HIS ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 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** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.165180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139257 restraints weight = 69753.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141711 restraints weight = 41414.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.143303 restraints weight = 28967.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.144422 restraints weight = 22960.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.145012 restraints weight = 19784.235| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.280 34887 Z= 0.256 Angle : 0.907 59.161 47340 Z= 0.489 Chirality : 0.048 0.645 5292 Planarity : 0.006 0.173 5936 Dihedral : 11.828 84.402 5111 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.89 % Favored : 91.03 % Rotamer: Outliers : 4.42 % Allowed : 24.72 % Favored : 70.86 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: -2.22 (0.13), residues: 4093 helix: -0.68 (0.14), residues: 1248 sheet: -1.48 (0.23), residues: 524 loop : -1.97 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 929 TYR 0.028 0.002 TYR A 697 PHE 0.062 0.002 PHE B 827 TRP 0.124 0.004 TRP B 832 HIS 0.009 0.001 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00534 (34863) covalent geometry : angle 0.89527 (47313) hydrogen bonds : bond 0.04083 ( 1105) hydrogen bonds : angle 5.78062 ( 3058) metal coordination : bond 0.02361 ( 23) metal coordination : angle 6.19983 ( 27) Misc. bond : bond 0.00218 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6787.90 seconds wall clock time: 118 minutes 36.25 seconds (7116.25 seconds total)