Starting phenix.real_space_refine on Sun Dec 29 22:00:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pe7_13347/12_2024/7pe7_13347.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pe7_13347/12_2024/7pe7_13347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pe7_13347/12_2024/7pe7_13347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pe7_13347/12_2024/7pe7_13347.map" model { file = "/net/cci-nas-00/data/ceres_data/7pe7_13347/12_2024/7pe7_13347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pe7_13347/12_2024/7pe7_13347.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.045 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 2 6.06 5 P 12 5.49 5 S 350 5.16 5 C 37076 2.51 5 N 10408 2.21 5 O 10734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 58582 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 16419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2194, 16419 Classifications: {'peptide': 2194} Incomplete info: {'truncation_to_alanine': 359} Link IDs: {'PTRANS': 88, 'TRANS': 2105} Chain breaks: 20 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1672 Unresolved non-hydrogen dihedrals: 1079 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 18, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 9, 'PHE:plan': 19, 'GLU:plan': 33, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 714 Chain: "C" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2465 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 8917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8917 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1077} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 655 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "I" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 55411 SG CYS E1520 25.630 124.627 204.184 1.00178.71 S ATOM 55437 SG CYS E1523 21.873 124.563 204.610 1.00196.92 S ATOM 55897 SG CYS E1651 23.546 127.849 203.544 1.00161.06 S Restraints were copied for chains: D, H, J, F, B Time building chain proxies: 61.39, per 1000 atoms: 1.05 Number of scatterers: 58582 At special positions: 0 Unit cell: (153.41, 207.368, 249.688, 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 2 29.99 S 350 16.00 P 12 15.00 O 10734 8.00 N 10408 7.00 C 37076 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.89 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E4801 " pdb="ZN ZN E4801 " - pdb=" NE2 HIS E1515 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1523 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1520 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1651 " pdb=" ZN F4801 " pdb="ZN ZN F4801 " - pdb=" NE2 HIS F1515 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1523 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1520 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1651 " Number of angles added : 6 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14620 Finding SS restraints... Secondary structure from input PDB file: 432 helices and 26 sheets defined 67.6% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.96 Creating SS restraints... Processing helix chain 'B' and resid 17 through 30 Processing helix chain 'B' and resid 38 through 53 Processing helix chain 'B' and resid 61 through 74 Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 101 through 115 removed outlier: 3.544A pdb=" N ARG B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 114 " --> pdb=" O TYR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 removed outlier: 4.068A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 156 Processing helix chain 'B' and resid 164 through 179 Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.606A pdb=" N GLN B 185 " --> pdb=" O PHE B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.787A pdb=" N GLU B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 246 Processing helix chain 'B' and resid 261 through 276 Processing helix chain 'B' and resid 277 through 289 removed outlier: 3.872A pdb=" N LEU B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 362 through 376 Processing helix chain 'B' and resid 387 through 403 Proline residue: B 397 - end of helix Processing helix chain 'B' and resid 411 through 425 removed outlier: 3.713A pdb=" N LYS B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 444 Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.915A pdb=" N VAL B 455 " --> pdb=" O TYR B 451 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.521A pdb=" N PHE B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 512 removed outlier: 4.285A pdb=" N GLU B 503 " --> pdb=" O GLN B 499 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Proline residue: B 507 - end of helix removed outlier: 3.991A pdb=" N GLY B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 528 Processing helix chain 'B' and resid 531 through 549 removed outlier: 4.311A pdb=" N HIS B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 590 removed outlier: 3.599A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 607 removed outlier: 3.658A pdb=" N ARG B 604 " --> pdb=" O THR B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 615 through 629 removed outlier: 3.662A pdb=" N ARG B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 621 " --> pdb=" O GLU B 617 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 624 " --> pdb=" O MET B 620 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B 627 " --> pdb=" O ALA B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 665 removed outlier: 3.587A pdb=" N SER B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 679 removed outlier: 3.742A pdb=" N ARG B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 686 removed outlier: 4.638A pdb=" N ALA B 685 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 701 removed outlier: 3.517A pdb=" N GLN B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 720 removed outlier: 3.542A pdb=" N LEU B 710 " --> pdb=" O GLU B 706 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER B 720 " --> pdb=" O GLY B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 743 Proline residue: B 728 - end of helix removed outlier: 4.024A pdb=" N LYS B 732 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 741 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 764 removed outlier: 3.518A pdb=" N MET B 756 " --> pdb=" O GLN B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 769 removed outlier: 3.607A pdb=" N ILE B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 784 removed outlier: 3.654A pdb=" N ILE B 775 " --> pdb=" O TYR B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 778 " --> pdb=" O PRO B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 809 removed outlier: 3.648A pdb=" N ASN B 797 " --> pdb=" O GLY B 793 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 800 " --> pdb=" O ASN B 796 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 804 " --> pdb=" O ALA B 800 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 807 " --> pdb=" O GLY B 803 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 829 removed outlier: 4.301A pdb=" N ILE B 822 " --> pdb=" O ASP B 818 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 827 " --> pdb=" O ILE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 847 removed outlier: 4.546A pdb=" N ALA B 840 " --> pdb=" O LYS B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 852 removed outlier: 3.645A pdb=" N THR B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 861 removed outlier: 3.645A pdb=" N LYS B 860 " --> pdb=" O GLU B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 875 removed outlier: 3.691A pdb=" N LEU B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS B 873 " --> pdb=" O LEU B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 892 removed outlier: 3.759A pdb=" N ARG B 886 " --> pdb=" O ARG B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 902 removed outlier: 3.507A pdb=" N HIS B 899 " --> pdb=" O ASP B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 937 removed outlier: 3.674A pdb=" N VAL B 936 " --> pdb=" O SER B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 958 removed outlier: 3.951A pdb=" N TYR B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Proline residue: B 948 - end of helix removed outlier: 3.784A pdb=" N ILE B 958 " --> pdb=" O ALA B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 966 removed outlier: 3.632A pdb=" N LEU B 964 " --> pdb=" O ASP B 961 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N HIS B 966 " --> pdb=" O SER B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 983 removed outlier: 3.903A pdb=" N VAL B 972 " --> pdb=" O HIS B 968 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN B 973 " --> pdb=" O THR B 969 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 977 " --> pdb=" O GLN B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 988 No H-bonds generated for 'chain 'B' and resid 986 through 988' Processing helix chain 'B' and resid 989 through 1004 Proline residue: B 995 - end of helix Processing helix chain 'B' and resid 1006 through 1020 removed outlier: 4.339A pdb=" N GLU B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B1014 " --> pdb=" O GLU B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1042 removed outlier: 3.504A pdb=" N ILE B1034 " --> pdb=" O TYR B1030 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B1040 " --> pdb=" O THR B1036 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE B1041 " --> pdb=" O LEU B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1064 removed outlier: 3.680A pdb=" N VAL B1061 " --> pdb=" O GLU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1073 removed outlier: 3.770A pdb=" N LEU B1071 " --> pdb=" O LYS B1068 " (cutoff:3.500A) Proline residue: B1072 - end of helix Processing helix chain 'B' and resid 1074 through 1080 removed outlier: 3.696A pdb=" N ARG B1080 " --> pdb=" O PRO B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1089 No H-bonds generated for 'chain 'B' and resid 1087 through 1089' Processing helix chain 'B' and resid 1090 through 1101 removed outlier: 4.008A pdb=" N ALA B1099 " --> pdb=" O LYS B1095 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B1101 " --> pdb=" O LEU B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1107 removed outlier: 6.020A pdb=" N ALA B1105 " --> pdb=" O LEU B1102 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B1107 " --> pdb=" O GLY B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1120 Proline residue: B1116 - end of helix Processing helix chain 'B' and resid 1128 through 1144 removed outlier: 3.722A pdb=" N VAL B1139 " --> pdb=" O ALA B1135 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP B1140 " --> pdb=" O LEU B1136 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU B1144 " --> pdb=" O ASP B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1164 removed outlier: 4.039A pdb=" N HIS B1157 " --> pdb=" O SER B1153 " (cutoff:3.500A) Proline residue: B1158 - end of helix removed outlier: 4.236A pdb=" N ASP B1164 " --> pdb=" O VAL B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1169 through 1182 removed outlier: 3.623A pdb=" N ASP B1175 " --> pdb=" O SER B1171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B1176 " --> pdb=" O THR B1172 " (cutoff:3.500A) Processing helix chain 'B' and resid 1185 through 1190 removed outlier: 3.960A pdb=" N TYR B1188 " --> pdb=" O GLY B1185 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B1190 " --> pdb=" O LYS B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1203 removed outlier: 3.524A pdb=" N LYS B1197 " --> pdb=" O PRO B1193 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B1198 " --> pdb=" O MET B1194 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B1201 " --> pdb=" O LYS B1197 " (cutoff:3.500A) Processing helix chain 'B' and resid 1206 through 1218 Processing helix chain 'B' and resid 1228 through 1238 Processing helix chain 'B' and resid 1264 through 1270 removed outlier: 3.865A pdb=" N ALA B1268 " --> pdb=" O ASN B1264 " (cutoff:3.500A) Processing helix chain 'B' and resid 1276 through 1294 removed outlier: 3.558A pdb=" N ASP B1294 " --> pdb=" O GLU B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1297 through 1302 Processing helix chain 'B' and resid 1303 through 1310 removed outlier: 3.663A pdb=" N ALA B1309 " --> pdb=" O ALA B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1311 through 1316 removed outlier: 4.022A pdb=" N ASP B1316 " --> pdb=" O PRO B1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1329 removed outlier: 3.872A pdb=" N GLU B1328 " --> pdb=" O SER B1324 " (cutoff:3.500A) Processing helix chain 'B' and resid 1330 through 1346 removed outlier: 3.645A pdb=" N GLU B1336 " --> pdb=" O ASP B1332 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B1337 " --> pdb=" O GLN B1333 " (cutoff:3.500A) Processing helix chain 'B' and resid 1350 through 1367 Processing helix chain 'B' and resid 1376 through 1378 No H-bonds generated for 'chain 'B' and resid 1376 through 1378' Processing helix chain 'B' and resid 1379 through 1387 Processing helix chain 'B' and resid 1392 through 1407 removed outlier: 3.513A pdb=" N ALA B1396 " --> pdb=" O ALA B1392 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B1398 " --> pdb=" O ALA B1394 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B1406 " --> pdb=" O LEU B1402 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B1407 " --> pdb=" O GLU B1403 " (cutoff:3.500A) Processing helix chain 'B' and resid 1409 through 1422 Processing helix chain 'B' and resid 1425 through 1439 removed outlier: 3.695A pdb=" N VAL B1432 " --> pdb=" O ALA B1428 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B1433 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B1438 " --> pdb=" O GLU B1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 1446 through 1453 removed outlier: 4.317A pdb=" N TYR B1450 " --> pdb=" O GLN B1446 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU B1451 " --> pdb=" O ALA B1447 " (cutoff:3.500A) Processing helix chain 'B' and resid 1456 through 1469 removed outlier: 3.863A pdb=" N VAL B1461 " --> pdb=" O GLU B1457 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B1466 " --> pdb=" O ALA B1462 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B1469 " --> pdb=" O LYS B1465 " (cutoff:3.500A) Processing helix chain 'B' and resid 1475 through 1488 removed outlier: 3.755A pdb=" N ALA B1486 " --> pdb=" O ARG B1482 " (cutoff:3.500A) Processing helix chain 'B' and resid 1489 through 1501 removed outlier: 3.613A pdb=" N GLN B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) Processing helix chain 'B' and resid 1505 through 1524 removed outlier: 3.897A pdb=" N LYS B1511 " --> pdb=" O GLU B1507 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B1512 " --> pdb=" O THR B1508 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG B1514 " --> pdb=" O ALA B1510 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET B1515 " --> pdb=" O LYS B1511 " (cutoff:3.500A) Processing helix chain 'B' and resid 1525 through 1534 removed outlier: 3.811A pdb=" N GLU B1530 " --> pdb=" O TRP B1526 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU B1531 " --> pdb=" O ASP B1527 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1554 removed outlier: 4.215A pdb=" N ARG B1547 " --> pdb=" O GLY B1543 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B1550 " --> pdb=" O TYR B1546 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B1552 " --> pdb=" O ALA B1548 " (cutoff:3.500A) Processing helix chain 'B' and resid 1556 through 1580 removed outlier: 3.771A pdb=" N GLN B1562 " --> pdb=" O SER B1558 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B1569 " --> pdb=" O ASP B1565 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B1570 " --> pdb=" O LYS B1566 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B1573 " --> pdb=" O ASP B1569 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU B1574 " --> pdb=" O LEU B1570 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B1577 " --> pdb=" O ALA B1573 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET B1578 " --> pdb=" O GLU B1574 " (cutoff:3.500A) Processing helix chain 'B' and resid 1584 through 1588 removed outlier: 3.585A pdb=" N TYR B1587 " --> pdb=" O SER B1584 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B1588 " --> pdb=" O ARG B1585 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1584 through 1588' Processing helix chain 'B' and resid 1589 through 1608 removed outlier: 3.651A pdb=" N GLU B1600 " --> pdb=" O LEU B1596 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B1601 " --> pdb=" O SER B1597 " (cutoff:3.500A) Processing helix chain 'B' and resid 1609 through 1612 removed outlier: 3.509A pdb=" N ARG B1612 " --> pdb=" O PRO B1609 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1609 through 1612' Processing helix chain 'B' and resid 1614 through 1624 removed outlier: 5.436A pdb=" N TRP B1620 " --> pdb=" O ARG B1616 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B1621 " --> pdb=" O GLN B1617 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B1623 " --> pdb=" O TRP B1619 " (cutoff:3.500A) Processing helix chain 'B' and resid 1629 through 1640 Processing helix chain 'B' and resid 1645 through 1648 Processing helix chain 'B' and resid 1649 through 1664 removed outlier: 3.949A pdb=" N TRP B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B1655 " --> pdb=" O ARG B1651 " (cutoff:3.500A) Processing helix chain 'B' and resid 1665 through 1678 removed outlier: 3.842A pdb=" N LEU B1673 " --> pdb=" O ALA B1669 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B1676 " --> pdb=" O THR B1672 " (cutoff:3.500A) Processing helix chain 'B' and resid 1693 through 1708 removed outlier: 3.517A pdb=" N LYS B1702 " --> pdb=" O TYR B1698 " (cutoff:3.500A) Processing helix chain 'B' and resid 1711 through 1729 removed outlier: 3.717A pdb=" N GLN B1725 " --> pdb=" O VAL B1721 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN B1726 " --> pdb=" O GLN B1722 " (cutoff:3.500A) Processing helix chain 'B' and resid 1738 through 1762 Processing helix chain 'B' and resid 1767 through 1783 removed outlier: 3.526A pdb=" N GLU B1781 " --> pdb=" O SER B1777 " (cutoff:3.500A) Processing helix chain 'B' and resid 1786 through 1809 removed outlier: 3.537A pdb=" N ALA B1792 " --> pdb=" O LYS B1788 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B1802 " --> pdb=" O PHE B1798 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B1809 " --> pdb=" O LYS B1805 " (cutoff:3.500A) Processing helix chain 'B' and resid 1877 through 1896 Proline residue: B1883 - end of helix removed outlier: 3.613A pdb=" N ARG B1896 " --> pdb=" O ILE B1892 " (cutoff:3.500A) Processing helix chain 'B' and resid 1899 through 1914 removed outlier: 3.544A pdb=" N VAL B1906 " --> pdb=" O ASP B1902 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B1907 " --> pdb=" O THR B1903 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B1908 " --> pdb=" O LEU B1904 " (cutoff:3.500A) Processing helix chain 'B' and resid 1916 through 1930 removed outlier: 3.549A pdb=" N ASN B1920 " --> pdb=" O TRP B1916 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B1921 " --> pdb=" O PRO B1917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B1922 " --> pdb=" O ASP B1918 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B1925 " --> pdb=" O GLU B1921 " (cutoff:3.500A) Processing helix chain 'B' and resid 1935 through 1937 No H-bonds generated for 'chain 'B' and resid 1935 through 1937' Processing helix chain 'B' and resid 1938 through 1945 removed outlier: 3.715A pdb=" N ARG B1945 " --> pdb=" O GLN B1941 " (cutoff:3.500A) Processing helix chain 'B' and resid 1950 through 1968 removed outlier: 4.391A pdb=" N LEU B1956 " --> pdb=" O LEU B1952 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B1957 " --> pdb=" O VAL B1953 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS B1958 " --> pdb=" O GLY B1954 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B1960 " --> pdb=" O LEU B1956 " (cutoff:3.500A) Processing helix chain 'B' and resid 1972 through 1981 Processing helix chain 'B' and resid 1984 through 1999 removed outlier: 3.575A pdb=" N ASN B1997 " --> pdb=" O LYS B1993 " (cutoff:3.500A) Processing helix chain 'B' and resid 2002 through 2021 removed outlier: 4.387A pdb=" N VAL B2006 " --> pdb=" O SER B2002 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B2021 " --> pdb=" O ILE B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2041 Processing helix chain 'B' and resid 2044 through 2059 removed outlier: 3.550A pdb=" N GLU B2049 " --> pdb=" O LYS B2045 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B2050 " --> pdb=" O GLY B2046 " (cutoff:3.500A) Proline residue: B2053 - end of helix removed outlier: 4.019A pdb=" N MET B2058 " --> pdb=" O LEU B2054 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B2059 " --> pdb=" O HIS B2055 " (cutoff:3.500A) Processing helix chain 'B' and resid 2064 through 2074 Processing helix chain 'B' and resid 2074 through 2091 removed outlier: 3.784A pdb=" N LYS B2090 " --> pdb=" O ARG B2086 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2113 removed outlier: 3.782A pdb=" N LEU B2097 " --> pdb=" O ASN B2093 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B2103 " --> pdb=" O GLN B2099 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS B2106 " --> pdb=" O ASP B2102 " (cutoff:3.500A) Processing helix chain 'B' and resid 2123 through 2127 Processing helix chain 'B' and resid 2192 through 2211 Processing helix chain 'B' and resid 2212 through 2217 removed outlier: 3.526A pdb=" N ARG B2217 " --> pdb=" O PRO B2213 " (cutoff:3.500A) Processing helix chain 'B' and resid 2246 through 2257 Processing helix chain 'B' and resid 2262 through 2272 Processing helix chain 'B' and resid 2274 through 2278 Processing helix chain 'B' and resid 2279 through 2294 removed outlier: 3.526A pdb=" N VAL B2284 " --> pdb=" O LEU B2280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B2285 " --> pdb=" O MET B2281 " (cutoff:3.500A) Processing helix chain 'B' and resid 2297 through 2306 removed outlier: 3.816A pdb=" N TRP B2304 " --> pdb=" O ALA B2300 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B2306 " --> pdb=" O LEU B2302 " (cutoff:3.500A) Processing helix chain 'B' and resid 2309 through 2335 removed outlier: 3.860A pdb=" N VAL B2326 " --> pdb=" O ARG B2322 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET B2327 " --> pdb=" O SER B2323 " (cutoff:3.500A) Processing helix chain 'B' and resid 2340 through 2342 No H-bonds generated for 'chain 'B' and resid 2340 through 2342' Processing helix chain 'B' and resid 2363 through 2368 removed outlier: 3.603A pdb=" N THR B2367 " --> pdb=" O GLU B2363 " (cutoff:3.500A) Processing helix chain 'B' and resid 2380 through 2385 Processing helix chain 'B' and resid 2394 through 2410 Processing helix chain 'B' and resid 2410 through 2423 removed outlier: 3.873A pdb=" N VAL B2417 " --> pdb=" O SER B2413 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B2418 " --> pdb=" O VAL B2414 " (cutoff:3.500A) Processing helix chain 'B' and resid 2428 through 2432 Processing helix chain 'B' and resid 2494 through 2508 removed outlier: 3.538A pdb=" N GLN B2499 " --> pdb=" O LYS B2495 " (cutoff:3.500A) Processing helix chain 'B' and resid 2520 through 2534 Processing helix chain 'B' and resid 2534 through 2540 removed outlier: 3.922A pdb=" N GLN B2540 " --> pdb=" O GLU B2536 " (cutoff:3.500A) Processing helix chain 'B' and resid 2542 through 2546 Processing helix chain 'F' and resid 32 through 44 removed outlier: 4.103A pdb=" N ARG F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 41 " --> pdb=" O ASN F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 52 through 70 removed outlier: 3.549A pdb=" N ASN F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP F 69 " --> pdb=" O LYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 90 removed outlier: 3.521A pdb=" N LEU F 90 " --> pdb=" O ILE F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 111 Processing helix chain 'F' and resid 113 through 123 removed outlier: 3.526A pdb=" N LEU F 123 " --> pdb=" O LYS F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.700A pdb=" N ARG F 131 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE F 133 " --> pdb=" O ILE F 129 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP F 134 " --> pdb=" O ALA F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 157 removed outlier: 3.510A pdb=" N GLN F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 161 removed outlier: 3.770A pdb=" N PHE F 161 " --> pdb=" O ALA F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 161' Processing helix chain 'F' and resid 162 through 175 removed outlier: 3.570A pdb=" N THR F 166 " --> pdb=" O PRO F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 198 removed outlier: 3.925A pdb=" N ILE F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.853A pdb=" N VAL F 202 " --> pdb=" O ASN F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 217 removed outlier: 3.782A pdb=" N THR F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 235 removed outlier: 3.670A pdb=" N ILE F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 244 Processing helix chain 'F' and resid 249 through 253 removed outlier: 3.616A pdb=" N ILE F 253 " --> pdb=" O LEU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 272 through 292 removed outlier: 3.602A pdb=" N GLU F 278 " --> pdb=" O LYS F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.569A pdb=" N ILE F 299 " --> pdb=" O TRP F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 303 removed outlier: 4.196A pdb=" N LYS F 303 " --> pdb=" O ASN F 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 300 through 303' Processing helix chain 'F' and resid 307 through 315 removed outlier: 3.669A pdb=" N SER F 311 " --> pdb=" O SER F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 318 No H-bonds generated for 'chain 'F' and resid 316 through 318' Processing helix chain 'F' and resid 320 through 336 removed outlier: 3.503A pdb=" N ARG F 324 " --> pdb=" O ASN F 320 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU F 329 " --> pdb=" O ARG F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 351 Processing helix chain 'F' and resid 359 through 363 removed outlier: 4.161A pdb=" N ARG F 363 " --> pdb=" O ASP F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 375 removed outlier: 4.236A pdb=" N THR F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 403 removed outlier: 3.525A pdb=" N ASN F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 414 Processing helix chain 'F' and resid 416 through 435 removed outlier: 3.662A pdb=" N VAL F 421 " --> pdb=" O ASP F 417 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG F 422 " --> pdb=" O HIS F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 455 removed outlier: 3.586A pdb=" N MET F 455 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 486 removed outlier: 3.534A pdb=" N HIS F 480 " --> pdb=" O LEU F 476 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU F 481 " --> pdb=" O LYS F 477 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET F 482 " --> pdb=" O ARG F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 507 removed outlier: 3.643A pdb=" N ILE F 497 " --> pdb=" O HIS F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 535 removed outlier: 3.534A pdb=" N LEU F 528 " --> pdb=" O THR F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 556 removed outlier: 3.840A pdb=" N THR F 553 " --> pdb=" O ASN F 549 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F 554 " --> pdb=" O LEU F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 581 removed outlier: 3.903A pdb=" N PHE F 580 " --> pdb=" O ARG F 576 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR F 581 " --> pdb=" O LEU F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 597 through 615 removed outlier: 3.775A pdb=" N PHE F 611 " --> pdb=" O GLN F 607 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER F 615 " --> pdb=" O PHE F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 638 removed outlier: 3.767A pdb=" N ASP F 625 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 626 " --> pdb=" O TYR F 622 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP F 629 " --> pdb=" O ASP F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 647 through 654 Processing helix chain 'F' and resid 655 through 658 Processing helix chain 'F' and resid 659 through 665 Processing helix chain 'F' and resid 666 through 668 No H-bonds generated for 'chain 'F' and resid 666 through 668' Processing helix chain 'F' and resid 669 through 680 removed outlier: 3.948A pdb=" N LYS F 674 " --> pdb=" O PRO F 670 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET F 675 " --> pdb=" O HIS F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 681 through 688 Processing helix chain 'F' and resid 695 through 703 removed outlier: 3.511A pdb=" N THR F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 711 through 723 removed outlier: 3.859A pdb=" N VAL F 715 " --> pdb=" O GLY F 711 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU F 717 " --> pdb=" O ALA F 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 735 Processing helix chain 'F' and resid 737 through 742 Processing helix chain 'F' and resid 746 through 751 removed outlier: 3.953A pdb=" N TRP F 750 " --> pdb=" O PHE F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 758 removed outlier: 3.665A pdb=" N THR F 757 " --> pdb=" O GLU F 753 " (cutoff:3.500A) Processing helix chain 'F' and resid 759 through 761 No H-bonds generated for 'chain 'F' and resid 759 through 761' Processing helix chain 'F' and resid 763 through 778 removed outlier: 3.617A pdb=" N GLU F 776 " --> pdb=" O ASP F 772 " (cutoff:3.500A) Processing helix chain 'F' and resid 780 through 791 Processing helix chain 'F' and resid 798 through 806 Processing helix chain 'F' and resid 807 through 810 Processing helix chain 'F' and resid 811 through 819 removed outlier: 3.536A pdb=" N TYR F 817 " --> pdb=" O LYS F 813 " (cutoff:3.500A) Processing helix chain 'F' and resid 823 through 834 Processing helix chain 'F' and resid 837 through 851 removed outlier: 3.648A pdb=" N ASP F 841 " --> pdb=" O SER F 837 " (cutoff:3.500A) Processing helix chain 'F' and resid 881 through 886 Processing helix chain 'F' and resid 889 through 899 removed outlier: 3.724A pdb=" N LEU F 895 " --> pdb=" O THR F 891 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 911 removed outlier: 3.618A pdb=" N ASN F 908 " --> pdb=" O GLU F 904 " (cutoff:3.500A) Processing helix chain 'F' and resid 916 through 934 removed outlier: 3.835A pdb=" N LYS F 921 " --> pdb=" O TRP F 917 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS F 922 " --> pdb=" O GLU F 918 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA F 929 " --> pdb=" O ALA F 925 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN F 932 " --> pdb=" O TRP F 928 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE F 933 " --> pdb=" O ALA F 929 " (cutoff:3.500A) Processing helix chain 'F' and resid 936 through 941 removed outlier: 3.527A pdb=" N ASN F 941 " --> pdb=" O ASN F 937 " (cutoff:3.500A) Processing helix chain 'F' and resid 948 through 956 Processing helix chain 'F' and resid 961 through 976 removed outlier: 3.900A pdb=" N VAL F 969 " --> pdb=" O ARG F 965 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR F 970 " --> pdb=" O GLY F 966 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 974 " --> pdb=" O TYR F 970 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE F 975 " --> pdb=" O VAL F 971 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F 976 " --> pdb=" O LEU F 972 " (cutoff:3.500A) Processing helix chain 'F' and resid 978 through 988 removed outlier: 3.563A pdb=" N ILE F 984 " --> pdb=" O GLN F 980 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS F 988 " --> pdb=" O ILE F 984 " (cutoff:3.500A) Processing helix chain 'F' and resid 1432 through 1436 removed outlier: 3.583A pdb=" N ILE F1436 " --> pdb=" O ILE F1433 " (cutoff:3.500A) Processing helix chain 'F' and resid 1480 through 1485 removed outlier: 4.097A pdb=" N GLN F1485 " --> pdb=" O HIS F1481 " (cutoff:3.500A) Processing helix chain 'F' and resid 1488 through 1494 removed outlier: 3.770A pdb=" N MET F1493 " --> pdb=" O LEU F1489 " (cutoff:3.500A) Processing helix chain 'F' and resid 1522 through 1526 Processing helix chain 'F' and resid 1609 through 1623 removed outlier: 3.647A pdb=" N ARG F1613 " --> pdb=" O ARG F1609 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS F1614 " --> pdb=" O ILE F1610 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU F1615 " --> pdb=" O LEU F1611 " (cutoff:3.500A) Processing helix chain 'F' and resid 1628 through 1643 removed outlier: 3.528A pdb=" N HIS F1632 " --> pdb=" O SER F1628 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE F1639 " --> pdb=" O GLY F1635 " (cutoff:3.500A) Processing helix chain 'F' and resid 1649 through 1663 removed outlier: 3.606A pdb=" N SER F1661 " --> pdb=" O SER F1657 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS F1662 " --> pdb=" O HIS F1658 " (cutoff:3.500A) Processing helix chain 'F' and resid 1666 through 1673 Processing helix chain 'F' and resid 1682 through 1694 Processing helix chain 'H' and resid 6 through 21 removed outlier: 3.521A pdb=" N ILE H 10 " --> pdb=" O ASN H 6 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA H 12 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL H 19 " --> pdb=" O ARG H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 31 Processing helix chain 'H' and resid 32 through 36 Processing helix chain 'H' and resid 85 through 100 removed outlier: 3.901A pdb=" N GLU H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 124 removed outlier: 4.009A pdb=" N PHE H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 61 through 74 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.545A pdb=" N ARG A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 135 removed outlier: 4.069A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 156 Processing helix chain 'A' and resid 164 through 179 Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.607A pdb=" N GLN A 185 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 198 Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.787A pdb=" N GLU A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.873A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 362 through 376 Processing helix chain 'A' and resid 387 through 403 Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 411 through 425 removed outlier: 3.713A pdb=" N LYS A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 Processing helix chain 'A' and resid 451 through 463 removed outlier: 3.914A pdb=" N VAL A 455 " --> pdb=" O TYR A 451 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 removed outlier: 3.520A pdb=" N PHE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 removed outlier: 4.285A pdb=" N GLU A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLU A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix removed outlier: 3.991A pdb=" N GLY A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 528 Processing helix chain 'A' and resid 531 through 549 removed outlier: 4.311A pdb=" N HIS A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 590 removed outlier: 3.599A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 607 removed outlier: 3.658A pdb=" N ARG A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.661A pdb=" N ARG A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 665 removed outlier: 3.587A pdb=" N SER A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 679 removed outlier: 3.742A pdb=" N ARG A 672 " --> pdb=" O ASP A 668 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 686 removed outlier: 4.638A pdb=" N ALA A 685 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 701 removed outlier: 3.518A pdb=" N GLN A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 720 removed outlier: 3.541A pdb=" N LEU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER A 720 " --> pdb=" O GLY A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 743 Proline residue: A 728 - end of helix removed outlier: 4.023A pdb=" N LYS A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 764 removed outlier: 3.518A pdb=" N MET A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 769 removed outlier: 3.606A pdb=" N ILE A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 784 removed outlier: 3.655A pdb=" N ILE A 775 " --> pdb=" O TYR A 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 809 removed outlier: 3.648A pdb=" N ASN A 797 " --> pdb=" O GLY A 793 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 829 removed outlier: 4.300A pdb=" N ILE A 822 " --> pdb=" O ASP A 818 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 847 removed outlier: 4.546A pdb=" N ALA A 840 " --> pdb=" O LYS A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 852 removed outlier: 3.644A pdb=" N THR A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 removed outlier: 3.644A pdb=" N LYS A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 875 removed outlier: 3.690A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 892 removed outlier: 3.759A pdb=" N ARG A 886 " --> pdb=" O ARG A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 902 removed outlier: 3.507A pdb=" N HIS A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 937 removed outlier: 3.674A pdb=" N VAL A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 958 removed outlier: 3.952A pdb=" N TYR A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Proline residue: A 948 - end of helix removed outlier: 3.784A pdb=" N ILE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.631A pdb=" N LEU A 964 " --> pdb=" O ASP A 961 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N HIS A 966 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 983 removed outlier: 3.903A pdb=" N VAL A 972 " --> pdb=" O HIS A 968 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN A 973 " --> pdb=" O THR A 969 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A 977 " --> pdb=" O GLN A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 988 No H-bonds generated for 'chain 'A' and resid 986 through 988' Processing helix chain 'A' and resid 989 through 1004 Proline residue: A 995 - end of helix Processing helix chain 'A' and resid 1006 through 1020 removed outlier: 4.339A pdb=" N GLU A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1042 removed outlier: 3.504A pdb=" N ILE A1034 " --> pdb=" O TYR A1030 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A1040 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1064 removed outlier: 3.679A pdb=" N VAL A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1073 removed outlier: 3.771A pdb=" N LEU A1071 " --> pdb=" O LYS A1068 " (cutoff:3.500A) Proline residue: A1072 - end of helix Processing helix chain 'A' and resid 1074 through 1080 removed outlier: 3.697A pdb=" N ARG A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'A' and resid 1090 through 1101 removed outlier: 4.007A pdb=" N ALA A1099 " --> pdb=" O LYS A1095 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A1101 " --> pdb=" O LEU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1107 removed outlier: 6.020A pdb=" N ALA A1105 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU A1107 " --> pdb=" O GLY A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1120 Proline residue: A1116 - end of helix Processing helix chain 'A' and resid 1128 through 1144 removed outlier: 3.723A pdb=" N VAL A1139 " --> pdb=" O ALA A1135 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A1140 " --> pdb=" O LEU A1136 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1164 removed outlier: 4.039A pdb=" N HIS A1157 " --> pdb=" O SER A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix removed outlier: 4.235A pdb=" N ASP A1164 " --> pdb=" O VAL A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1182 removed outlier: 3.623A pdb=" N ASP A1175 " --> pdb=" O SER A1171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A1176 " --> pdb=" O THR A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1190 removed outlier: 3.960A pdb=" N TYR A1188 " --> pdb=" O GLY A1185 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1203 removed outlier: 3.524A pdb=" N LYS A1197 " --> pdb=" O PRO A1193 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A1198 " --> pdb=" O MET A1194 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A1201 " --> pdb=" O LYS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1218 Processing helix chain 'A' and resid 1228 through 1238 Processing helix chain 'A' and resid 1264 through 1270 removed outlier: 3.866A pdb=" N ALA A1268 " --> pdb=" O ASN A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1294 removed outlier: 3.557A pdb=" N ASP A1294 " --> pdb=" O GLU A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1302 Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 3.663A pdb=" N ALA A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1316 removed outlier: 4.023A pdb=" N ASP A1316 " --> pdb=" O PRO A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1329 removed outlier: 3.872A pdb=" N GLU A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1346 removed outlier: 3.646A pdb=" N GLU A1336 " --> pdb=" O ASP A1332 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A1337 " --> pdb=" O GLN A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1367 Processing helix chain 'A' and resid 1376 through 1378 No H-bonds generated for 'chain 'A' and resid 1376 through 1378' Processing helix chain 'A' and resid 1379 through 1387 Processing helix chain 'A' and resid 1392 through 1407 removed outlier: 3.513A pdb=" N ALA A1396 " --> pdb=" O ALA A1392 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A1398 " --> pdb=" O ALA A1394 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A1406 " --> pdb=" O LEU A1402 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A1407 " --> pdb=" O GLU A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1422 Processing helix chain 'A' and resid 1425 through 1439 removed outlier: 3.696A pdb=" N VAL A1432 " --> pdb=" O ALA A1428 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1433 " --> pdb=" O ALA A1429 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A1438 " --> pdb=" O GLU A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 4.317A pdb=" N TYR A1450 " --> pdb=" O GLN A1446 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A1451 " --> pdb=" O ALA A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1456 through 1469 removed outlier: 3.862A pdb=" N VAL A1461 " --> pdb=" O GLU A1457 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A1466 " --> pdb=" O ALA A1462 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A1469 " --> pdb=" O LYS A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1488 removed outlier: 3.757A pdb=" N ALA A1486 " --> pdb=" O ARG A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1501 removed outlier: 3.613A pdb=" N GLN A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1524 removed outlier: 3.898A pdb=" N LYS A1511 " --> pdb=" O GLU A1507 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A1512 " --> pdb=" O THR A1508 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1534 removed outlier: 3.811A pdb=" N GLU A1530 " --> pdb=" O TRP A1526 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU A1531 " --> pdb=" O ASP A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1554 removed outlier: 4.215A pdb=" N ARG A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A1550 " --> pdb=" O TYR A1546 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A1552 " --> pdb=" O ALA A1548 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1580 removed outlier: 3.771A pdb=" N GLN A1562 " --> pdb=" O SER A1558 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A1569 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1570 " --> pdb=" O LYS A1566 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A1577 " --> pdb=" O ALA A1573 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET A1578 " --> pdb=" O GLU A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1588 removed outlier: 3.585A pdb=" N TYR A1587 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A1588 " --> pdb=" O ARG A1585 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1584 through 1588' Processing helix chain 'A' and resid 1589 through 1608 removed outlier: 3.651A pdb=" N GLU A1600 " --> pdb=" O LEU A1596 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A1601 " --> pdb=" O SER A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1612 removed outlier: 3.509A pdb=" N ARG A1612 " --> pdb=" O PRO A1609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1609 through 1612' Processing helix chain 'A' and resid 1614 through 1624 removed outlier: 5.437A pdb=" N TRP A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A1621 " --> pdb=" O GLN A1617 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1623 " --> pdb=" O TRP A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1640 Processing helix chain 'A' and resid 1645 through 1648 Processing helix chain 'A' and resid 1649 through 1664 removed outlier: 3.949A pdb=" N TRP A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS A1655 " --> pdb=" O ARG A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1678 removed outlier: 3.843A pdb=" N LEU A1673 " --> pdb=" O ALA A1669 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A1676 " --> pdb=" O THR A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1708 removed outlier: 3.517A pdb=" N LYS A1702 " --> pdb=" O TYR A1698 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1729 removed outlier: 3.715A pdb=" N GLN A1725 " --> pdb=" O VAL A1721 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A1726 " --> pdb=" O GLN A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1762 Processing helix chain 'A' and resid 1767 through 1783 removed outlier: 3.526A pdb=" N GLU A1781 " --> pdb=" O SER A1777 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1809 removed outlier: 3.536A pdb=" N ALA A1792 " --> pdb=" O LYS A1788 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A1802 " --> pdb=" O PHE A1798 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A1809 " --> pdb=" O LYS A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1877 through 1896 Proline residue: A1883 - end of helix removed outlier: 3.614A pdb=" N ARG A1896 " --> pdb=" O ILE A1892 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1914 removed outlier: 3.544A pdb=" N VAL A1906 " --> pdb=" O ASP A1902 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A1907 " --> pdb=" O THR A1903 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A1908 " --> pdb=" O LEU A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1916 through 1930 removed outlier: 3.550A pdb=" N ASN A1920 " --> pdb=" O TRP A1916 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A1921 " --> pdb=" O PRO A1917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA A1922 " --> pdb=" O ASP A1918 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A1925 " --> pdb=" O GLU A1921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1937 No H-bonds generated for 'chain 'A' and resid 1935 through 1937' Processing helix chain 'A' and resid 1938 through 1945 removed outlier: 3.715A pdb=" N ARG A1945 " --> pdb=" O GLN A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1968 removed outlier: 4.391A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A1957 " --> pdb=" O VAL A1953 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A1958 " --> pdb=" O GLY A1954 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A1960 " --> pdb=" O LEU A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1981 Processing helix chain 'A' and resid 1984 through 1999 removed outlier: 3.576A pdb=" N ASN A1997 " --> pdb=" O LYS A1993 " (cutoff:3.500A) Processing helix chain 'A' and resid 2002 through 2021 removed outlier: 4.387A pdb=" N VAL A2006 " --> pdb=" O SER A2002 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A2021 " --> pdb=" O ILE A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2041 Processing helix chain 'A' and resid 2044 through 2059 removed outlier: 3.549A pdb=" N GLU A2049 " --> pdb=" O LYS A2045 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A2050 " --> pdb=" O GLY A2046 " (cutoff:3.500A) Proline residue: A2053 - end of helix removed outlier: 4.020A pdb=" N MET A2058 " --> pdb=" O LEU A2054 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A2059 " --> pdb=" O HIS A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2064 through 2074 Processing helix chain 'A' and resid 2074 through 2091 removed outlier: 3.785A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2113 removed outlier: 3.781A pdb=" N LEU A2097 " --> pdb=" O ASN A2093 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A2103 " --> pdb=" O GLN A2099 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A2106 " --> pdb=" O ASP A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2127 Processing helix chain 'A' and resid 2192 through 2211 Processing helix chain 'A' and resid 2212 through 2217 removed outlier: 3.527A pdb=" N ARG A2217 " --> pdb=" O PRO A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2246 through 2257 Processing helix chain 'A' and resid 2262 through 2272 Processing helix chain 'A' and resid 2274 through 2278 Processing helix chain 'A' and resid 2279 through 2294 removed outlier: 3.526A pdb=" N VAL A2284 " --> pdb=" O LEU A2280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A2285 " --> pdb=" O MET A2281 " (cutoff:3.500A) Processing helix chain 'A' and resid 2297 through 2306 removed outlier: 3.816A pdb=" N TRP A2304 " --> pdb=" O ALA A2300 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A2306 " --> pdb=" O LEU A2302 " (cutoff:3.500A) Processing helix chain 'A' and resid 2309 through 2335 removed outlier: 3.859A pdb=" N VAL A2326 " --> pdb=" O ARG A2322 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A2327 " --> pdb=" O SER A2323 " (cutoff:3.500A) Processing helix chain 'A' and resid 2340 through 2342 No H-bonds generated for 'chain 'A' and resid 2340 through 2342' Processing helix chain 'A' and resid 2363 through 2368 removed outlier: 3.604A pdb=" N THR A2367 " --> pdb=" O GLU A2363 " (cutoff:3.500A) Processing helix chain 'A' and resid 2380 through 2385 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2410 through 2423 removed outlier: 3.873A pdb=" N VAL A2417 " --> pdb=" O SER A2413 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A2418 " --> pdb=" O VAL A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2428 through 2432 Processing helix chain 'A' and resid 2494 through 2508 removed outlier: 3.538A pdb=" N GLN A2499 " --> pdb=" O LYS A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2534 Processing helix chain 'A' and resid 2534 through 2540 removed outlier: 3.923A pdb=" N GLN A2540 " --> pdb=" O GLU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2546 Processing helix chain 'E' and resid 32 through 44 removed outlier: 4.102A pdb=" N ARG E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE E 41 " --> pdb=" O ASN E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 52 through 70 removed outlier: 3.549A pdb=" N ASN E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 90 removed outlier: 3.521A pdb=" N LEU E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 111 Processing helix chain 'E' and resid 113 through 123 removed outlier: 3.526A pdb=" N LEU E 123 " --> pdb=" O LYS E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 134 removed outlier: 3.700A pdb=" N ARG E 131 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE E 133 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP E 134 " --> pdb=" O ALA E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 157 removed outlier: 3.512A pdb=" N GLN E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 161 removed outlier: 3.770A pdb=" N PHE E 161 " --> pdb=" O ALA E 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 158 through 161' Processing helix chain 'E' and resid 162 through 175 removed outlier: 3.569A pdb=" N THR E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 198 removed outlier: 3.924A pdb=" N ILE E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.852A pdb=" N VAL E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 217 removed outlier: 3.782A pdb=" N THR E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 235 removed outlier: 3.671A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 244 Processing helix chain 'E' and resid 249 through 253 removed outlier: 3.616A pdb=" N ILE E 253 " --> pdb=" O LEU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 272 through 292 removed outlier: 3.603A pdb=" N GLU E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 299 removed outlier: 3.569A pdb=" N ILE E 299 " --> pdb=" O TRP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 303 removed outlier: 4.197A pdb=" N LYS E 303 " --> pdb=" O ASN E 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 300 through 303' Processing helix chain 'E' and resid 307 through 315 removed outlier: 3.668A pdb=" N SER E 311 " --> pdb=" O SER E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 320 through 336 removed outlier: 3.504A pdb=" N ARG E 324 " --> pdb=" O ASN E 320 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 329 " --> pdb=" O ARG E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 351 Processing helix chain 'E' and resid 359 through 363 removed outlier: 4.161A pdb=" N ARG E 363 " --> pdb=" O ASP E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 375 removed outlier: 4.237A pdb=" N THR E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 403 removed outlier: 3.525A pdb=" N ASN E 390 " --> pdb=" O ASP E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 414 Processing helix chain 'E' and resid 416 through 435 removed outlier: 3.662A pdb=" N VAL E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG E 422 " --> pdb=" O HIS E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 455 removed outlier: 3.586A pdb=" N MET E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 486 removed outlier: 3.534A pdb=" N HIS E 480 " --> pdb=" O LEU E 476 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU E 481 " --> pdb=" O LYS E 477 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET E 482 " --> pdb=" O ARG E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 507 removed outlier: 3.644A pdb=" N ILE E 497 " --> pdb=" O HIS E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.534A pdb=" N LEU E 528 " --> pdb=" O THR E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 556 removed outlier: 3.840A pdb=" N THR E 553 " --> pdb=" O ASN E 549 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE E 554 " --> pdb=" O LEU E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 581 removed outlier: 3.903A pdb=" N PHE E 580 " --> pdb=" O ARG E 576 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR E 581 " --> pdb=" O LEU E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 615 removed outlier: 3.777A pdb=" N PHE E 611 " --> pdb=" O GLN E 607 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER E 615 " --> pdb=" O PHE E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 638 removed outlier: 3.767A pdb=" N ASP E 625 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU E 626 " --> pdb=" O TYR E 622 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP E 629 " --> pdb=" O ASP E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 654 Processing helix chain 'E' and resid 655 through 658 Processing helix chain 'E' and resid 659 through 665 Processing helix chain 'E' and resid 666 through 668 No H-bonds generated for 'chain 'E' and resid 666 through 668' Processing helix chain 'E' and resid 669 through 680 removed outlier: 3.948A pdb=" N LYS E 674 " --> pdb=" O PRO E 670 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET E 675 " --> pdb=" O HIS E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 688 Processing helix chain 'E' and resid 695 through 703 removed outlier: 3.511A pdb=" N THR E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 711 through 723 removed outlier: 3.859A pdb=" N VAL E 715 " --> pdb=" O GLY E 711 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 717 " --> pdb=" O ALA E 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 735 Processing helix chain 'E' and resid 737 through 742 Processing helix chain 'E' and resid 746 through 751 removed outlier: 3.953A pdb=" N TRP E 750 " --> pdb=" O PHE E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 751 through 758 removed outlier: 3.665A pdb=" N THR E 757 " --> pdb=" O GLU E 753 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 761 No H-bonds generated for 'chain 'E' and resid 759 through 761' Processing helix chain 'E' and resid 763 through 778 removed outlier: 3.618A pdb=" N GLU E 776 " --> pdb=" O ASP E 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 780 through 791 Processing helix chain 'E' and resid 798 through 806 Processing helix chain 'E' and resid 807 through 810 Processing helix chain 'E' and resid 811 through 819 removed outlier: 3.535A pdb=" N TYR E 817 " --> pdb=" O LYS E 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 823 through 834 Processing helix chain 'E' and resid 837 through 851 removed outlier: 3.649A pdb=" N ASP E 841 " --> pdb=" O SER E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 881 through 886 Processing helix chain 'E' and resid 889 through 899 removed outlier: 3.723A pdb=" N LEU E 895 " --> pdb=" O THR E 891 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 911 removed outlier: 3.619A pdb=" N ASN E 908 " --> pdb=" O GLU E 904 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 934 removed outlier: 3.836A pdb=" N LYS E 921 " --> pdb=" O TRP E 917 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 929 " --> pdb=" O ALA E 925 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN E 932 " --> pdb=" O TRP E 928 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE E 933 " --> pdb=" O ALA E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 936 through 941 removed outlier: 3.528A pdb=" N ASN E 941 " --> pdb=" O ASN E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 948 through 956 Processing helix chain 'E' and resid 961 through 976 removed outlier: 3.900A pdb=" N VAL E 969 " --> pdb=" O ARG E 965 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR E 970 " --> pdb=" O GLY E 966 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 974 " --> pdb=" O TYR E 970 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE E 975 " --> pdb=" O VAL E 971 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 976 " --> pdb=" O LEU E 972 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 988 removed outlier: 3.563A pdb=" N ILE E 984 " --> pdb=" O GLN E 980 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS E 988 " --> pdb=" O ILE E 984 " (cutoff:3.500A) Processing helix chain 'E' and resid 1432 through 1436 removed outlier: 3.583A pdb=" N ILE E1436 " --> pdb=" O ILE E1433 " (cutoff:3.500A) Processing helix chain 'E' and resid 1480 through 1485 removed outlier: 4.097A pdb=" N GLN E1485 " --> pdb=" O HIS E1481 " (cutoff:3.500A) Processing helix chain 'E' and resid 1488 through 1494 removed outlier: 3.769A pdb=" N MET E1493 " --> pdb=" O LEU E1489 " (cutoff:3.500A) Processing helix chain 'E' and resid 1522 through 1526 Processing helix chain 'E' and resid 1609 through 1623 removed outlier: 3.647A pdb=" N ARG E1613 " --> pdb=" O ARG E1609 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS E1614 " --> pdb=" O ILE E1610 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E1615 " --> pdb=" O LEU E1611 " (cutoff:3.500A) Processing helix chain 'E' and resid 1628 through 1643 removed outlier: 3.527A pdb=" N HIS E1632 " --> pdb=" O SER E1628 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE E1639 " --> pdb=" O GLY E1635 " (cutoff:3.500A) Processing helix chain 'E' and resid 1649 through 1663 removed outlier: 3.606A pdb=" N SER E1661 " --> pdb=" O SER E1657 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS E1662 " --> pdb=" O HIS E1658 " (cutoff:3.500A) Processing helix chain 'E' and resid 1666 through 1673 Processing helix chain 'E' and resid 1682 through 1694 Processing helix chain 'G' and resid 6 through 21 removed outlier: 3.520A pdb=" N ILE G 10 " --> pdb=" O ASN G 6 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA G 12 " --> pdb=" O THR G 8 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 31 Processing helix chain 'G' and resid 32 through 36 Processing helix chain 'G' and resid 85 through 100 removed outlier: 3.901A pdb=" N GLU G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN G 99 " --> pdb=" O LYS G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 124 removed outlier: 4.009A pdb=" N PHE G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 364 Processing helix chain 'I' and resid 384 through 395 Processing helix chain 'J' and resid 359 through 364 Processing helix chain 'J' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'B' and resid 2120 through 2122 removed outlier: 3.830A pdb=" N GLN B2161 " --> pdb=" O LYS B2171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2153 through 2156 removed outlier: 6.811A pdb=" N MET B2175 " --> pdb=" O GLN B2154 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE B2156 " --> pdb=" O THR B2173 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR B2173 " --> pdb=" O ILE B2156 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B2182 " --> pdb=" O LEU B2174 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B2187 " --> pdb=" O GLY B2235 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B2235 " --> pdb=" O LYS B2187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2243 through 2245 removed outlier: 3.537A pdb=" N ASP B2244 " --> pdb=" O LEU B2346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 36 through 39 removed outlier: 3.936A pdb=" N ARG D 36 " --> pdb=" O PHE D 26 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N THR D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY D 19 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 321 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS D 317 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 47 through 50 removed outlier: 4.122A pdb=" N ALA D 47 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA D 60 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE D 79 " --> pdb=" O MET D 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 88 through 93 removed outlier: 6.661A pdb=" N GLY D 103 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL D 91 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR D 101 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE D 93 " --> pdb=" O TRP D 99 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP D 99 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 131 through 136 removed outlier: 3.718A pdb=" N CYS D 133 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 173 through 178 removed outlier: 3.966A pdb=" N SER D 175 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N CYS D 194 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS D 215 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL D 196 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 211 " --> pdb=" O ASN D 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 226 through 228 removed outlier: 3.569A pdb=" N LYS D 245 " --> pdb=" O THR D 237 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 256 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG D 248 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU D 254 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.603A pdb=" N ARG D 306 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 990 through 992 Processing sheet with id=AB3, first strand: chain 'A' and resid 2120 through 2122 removed outlier: 3.829A pdb=" N GLN A2161 " --> pdb=" O LYS A2171 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2153 through 2156 removed outlier: 6.811A pdb=" N MET A2175 " --> pdb=" O GLN A2154 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE A2156 " --> pdb=" O THR A2173 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR A2173 " --> pdb=" O ILE A2156 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A2182 " --> pdb=" O LEU A2174 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A2187 " --> pdb=" O GLY A2235 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A2235 " --> pdb=" O LYS A2187 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2243 through 2245 removed outlier: 3.537A pdb=" N ASP A2244 " --> pdb=" O LEU A2346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 36 through 39 removed outlier: 3.936A pdb=" N ARG C 36 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N THR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY C 19 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN C 321 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS C 317 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 47 through 50 removed outlier: 4.123A pdb=" N ALA C 47 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 60 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 88 through 93 removed outlier: 6.662A pdb=" N GLY C 103 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL C 91 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR C 101 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE C 93 " --> pdb=" O TRP C 99 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP C 99 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 131 through 136 removed outlier: 3.717A pdb=" N CYS C 133 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 173 through 178 removed outlier: 3.967A pdb=" N SER C 175 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS C 194 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS C 215 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL C 196 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 211 " --> pdb=" O ASN C 198 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 226 through 228 removed outlier: 3.568A pdb=" N LYS C 245 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 256 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.603A pdb=" N ARG C 306 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 990 through 992 Processing sheet with id=AC5, first strand: chain 'I' and resid 329 through 333 removed outlier: 4.888A pdb=" N SER I 374 " --> pdb=" O GLU I 402 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 342 through 344 removed outlier: 6.712A pdb=" N VAL I 343 " --> pdb=" O GLN I 353 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 329 through 333 removed outlier: 4.888A pdb=" N SER J 374 " --> pdb=" O GLU J 402 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 342 through 344 removed outlier: 6.713A pdb=" N VAL J 343 " --> pdb=" O GLN J 353 " (cutoff:3.500A) 3093 hydrogen bonds defined for protein. 9057 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.28 Time building geometry restraints manager: 12.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 19666 1.34 - 1.46: 12678 1.46 - 1.58: 26756 1.58 - 1.70: 12 1.70 - 1.81: 546 Bond restraints: 59658 Sorted by residual: bond pdb=" O12 IHP B2601 " pdb=" P2 IHP B2601 " ideal model delta sigma weight residual 1.675 1.598 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O12 IHP A2601 " pdb=" P2 IHP A2601 " ideal model delta sigma weight residual 1.675 1.598 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 1.671 1.601 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O14 IHP B2601 " pdb=" P4 IHP B2601 " ideal model delta sigma weight residual 1.671 1.601 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O15 IHP B2601 " pdb=" P5 IHP B2601 " ideal model delta sigma weight residual 1.675 1.619 0.056 2.00e-02 2.50e+03 7.94e+00 ... (remaining 59653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 80134 1.76 - 3.52: 712 3.52 - 5.28: 119 5.28 - 7.03: 19 7.03 - 8.79: 8 Bond angle restraints: 80992 Sorted by residual: angle pdb=" N VAL B1081 " pdb=" CA VAL B1081 " pdb=" C VAL B1081 " ideal model delta sigma weight residual 113.53 107.67 5.86 9.80e-01 1.04e+00 3.57e+01 angle pdb=" N VAL A1081 " pdb=" CA VAL A1081 " pdb=" C VAL A1081 " ideal model delta sigma weight residual 113.53 107.69 5.84 9.80e-01 1.04e+00 3.56e+01 angle pdb=" N ALA E 91 " pdb=" CA ALA E 91 " pdb=" C ALA E 91 " ideal model delta sigma weight residual 114.56 109.67 4.89 1.27e+00 6.20e-01 1.48e+01 angle pdb=" N THR B1934 " pdb=" CA THR B1934 " pdb=" C THR B1934 " ideal model delta sigma weight residual 114.56 109.70 4.86 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N THR A1934 " pdb=" CA THR A1934 " pdb=" C THR A1934 " ideal model delta sigma weight residual 114.56 109.70 4.86 1.27e+00 6.20e-01 1.46e+01 ... (remaining 80987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 34752 17.98 - 35.95: 1151 35.95 - 53.93: 157 53.93 - 71.91: 22 71.91 - 89.88: 12 Dihedral angle restraints: 36094 sinusoidal: 13684 harmonic: 22410 Sorted by residual: dihedral pdb=" CA TRP E 557 " pdb=" C TRP E 557 " pdb=" N PRO E 558 " pdb=" CA PRO E 558 " ideal model delta harmonic sigma weight residual -180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA TRP F 557 " pdb=" C TRP F 557 " pdb=" N PRO F 558 " pdb=" CA PRO F 558 " ideal model delta harmonic sigma weight residual 180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ARG E 833 " pdb=" C ARG E 833 " pdb=" N GLU E 834 " pdb=" CA GLU E 834 " ideal model delta harmonic sigma weight residual -180.00 -162.73 -17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 36091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 8356 0.057 - 0.113: 994 0.113 - 0.170: 44 0.170 - 0.226: 2 0.226 - 0.283: 4 Chirality restraints: 9400 Sorted by residual: chirality pdb=" C1 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O11 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.32 2.60 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1 IHP B2601 " pdb=" C2 IHP B2601 " pdb=" C6 IHP B2601 " pdb=" O11 IHP B2601 " both_signs ideal model delta sigma weight residual False 2.32 2.60 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C3 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C4 IHP A2601 " pdb=" O13 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.34 -2.59 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 9397 not shown) Planarity restraints: 10390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1689 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A1690 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A1690 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1690 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B1689 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO B1690 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B1690 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B1690 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1645 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO A1646 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1646 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1646 " 0.020 5.00e-02 4.00e+02 ... (remaining 10387 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5460 2.74 - 3.28: 59488 3.28 - 3.82: 90877 3.82 - 4.36: 108595 4.36 - 4.90: 187296 Nonbonded interactions: 451716 Sorted by model distance: nonbonded pdb=" OG1 THR C 51 " pdb=" O MET C 56 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR D 51 " pdb=" O MET D 56 " model vdw 2.205 3.040 nonbonded pdb=" O LEU B1343 " pdb=" OG SER B1347 " model vdw 2.215 3.040 nonbonded pdb=" O LEU A1343 " pdb=" OG SER A1347 " model vdw 2.216 3.040 nonbonded pdb=" OE2 GLU B2526 " pdb=" NZ LYS B2530 " model vdw 2.234 3.120 ... (remaining 451711 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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 individual isotropic 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: 8.050 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: 0.070 Extract box with map and model: 1.880 Check model and map are aligned: 0.350 Set scattering table: 0.410 Process input model: 147.910 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.002 0.077 59658 Z= 0.141 Angle : 0.458 8.794 80992 Z= 0.248 Chirality : 0.037 0.283 9400 Planarity : 0.003 0.055 10390 Dihedral : 9.059 89.885 21474 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 0.98 % Allowed : 4.03 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.10), residues: 7536 helix: 0.57 (0.08), residues: 4588 sheet: 0.12 (0.28), residues: 358 loop : -0.95 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 750 HIS 0.003 0.000 HIS E 445 PHE 0.011 0.001 PHE B1122 TYR 0.010 0.001 TYR E 835 ARG 0.003 0.000 ARG E 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1568 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 1510 time to evaluate : 5.145 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: B 631 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7053 (p) REVERT: B 725 PHE cc_start: 0.6807 (m-80) cc_final: 0.6582 (m-80) REVERT: B 772 MET cc_start: 0.8535 (mmp) cc_final: 0.8279 (mmm) REVERT: B 827 MET cc_start: 0.8418 (mtt) cc_final: 0.8211 (mtp) REVERT: B 956 MET cc_start: 0.8343 (mmm) cc_final: 0.7973 (mmm) REVERT: B 1227 GLU cc_start: 0.8042 (tp30) cc_final: 0.7776 (tt0) REVERT: B 1285 ARG cc_start: 0.7246 (ptm-80) cc_final: 0.7020 (ttp80) REVERT: B 1377 ASP cc_start: 0.6038 (t70) cc_final: 0.5694 (t70) REVERT: B 1539 ASP cc_start: 0.7792 (t0) cc_final: 0.7497 (t0) REVERT: B 1654 LEU cc_start: 0.8776 (mt) cc_final: 0.8541 (mt) REVERT: B 1726 GLN cc_start: 0.8651 (mp-120) cc_final: 0.8434 (mp10) REVERT: B 1747 MET cc_start: 0.8685 (mmm) cc_final: 0.8340 (mmm) REVERT: B 1757 TRP cc_start: 0.8660 (m-10) cc_final: 0.8375 (m-10) REVERT: B 1876 THR cc_start: 0.8152 (p) cc_final: 0.7669 (p) REVERT: B 1899 ASN cc_start: 0.8649 (p0) cc_final: 0.8171 (p0) REVERT: B 2063 GLN cc_start: 0.7578 (mp10) cc_final: 0.7285 (mp10) REVERT: B 2102 ASP cc_start: 0.7892 (t0) cc_final: 0.7466 (t0) REVERT: B 2135 ASP cc_start: 0.8468 (t0) cc_final: 0.8168 (t0) REVERT: B 2240 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8864 (m) REVERT: B 2514 SER cc_start: 0.7706 (t) cc_final: 0.7368 (p) REVERT: D 69 ASP cc_start: 0.7833 (t0) cc_final: 0.7432 (p0) REVERT: D 94 HIS cc_start: 0.6281 (t-90) cc_final: 0.5667 (t70) REVERT: D 124 ILE cc_start: 0.6939 (mt) cc_final: 0.6579 (mm) REVERT: D 166 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8088 (mt) REVERT: D 168 GLU cc_start: 0.7630 (pt0) cc_final: 0.7385 (pt0) REVERT: D 254 LEU cc_start: 0.8664 (mt) cc_final: 0.8414 (tp) REVERT: D 278 PHE cc_start: 0.7559 (m-80) cc_final: 0.7168 (m-10) REVERT: D 284 TYR cc_start: 0.6947 (m-80) cc_final: 0.6337 (m-80) REVERT: F 60 LEU cc_start: 0.7513 (mt) cc_final: 0.7094 (mt) REVERT: F 104 LEU cc_start: 0.8045 (mt) cc_final: 0.7595 (mm) REVERT: F 177 LEU cc_start: 0.8657 (tp) cc_final: 0.8452 (mp) REVERT: F 251 GLU cc_start: 0.7934 (mp0) cc_final: 0.7716 (mp0) REVERT: F 433 MET cc_start: 0.8189 (ttm) cc_final: 0.7976 (ttm) REVERT: F 482 MET cc_start: 0.8148 (ttp) cc_final: 0.7877 (ttm) REVERT: F 746 PHE cc_start: 0.7472 (m-10) cc_final: 0.7046 (m-10) REVERT: H 94 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7720 (ttm170) REVERT: A 680 ASP cc_start: 0.8097 (p0) cc_final: 0.7769 (t0) REVERT: A 796 ASN cc_start: 0.8061 (m-40) cc_final: 0.7767 (m-40) REVERT: A 1269 TRP cc_start: 0.7854 (m100) cc_final: 0.7519 (m100) REVERT: A 1332 ASP cc_start: 0.8156 (m-30) cc_final: 0.7811 (p0) REVERT: A 1350 ILE cc_start: 0.8360 (mp) cc_final: 0.7826 (tp) REVERT: A 1391 ARG cc_start: 0.7642 (mmt90) cc_final: 0.7207 (mtp85) REVERT: A 1503 LEU cc_start: 0.7919 (pt) cc_final: 0.7682 (pp) REVERT: A 1724 MET cc_start: 0.9062 (mmp) cc_final: 0.8579 (mmm) REVERT: A 1739 HIS cc_start: 0.7726 (t-90) cc_final: 0.7408 (t-90) REVERT: A 1960 LEU cc_start: 0.8739 (pp) cc_final: 0.8483 (pp) REVERT: A 2356 ILE cc_start: 0.8921 (pt) cc_final: 0.8701 (pt) REVERT: A 2404 MET cc_start: 0.8538 (mmt) cc_final: 0.8089 (tpt) REVERT: A 2514 SER cc_start: 0.7638 (t) cc_final: 0.7269 (p) REVERT: C 41 GLN cc_start: 0.7980 (tp40) cc_final: 0.7758 (pm20) REVERT: C 51 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7250 (p) REVERT: C 81 TYR cc_start: 0.7082 (m-80) cc_final: 0.6750 (m-80) REVERT: C 184 TYR cc_start: 0.5114 (m-80) cc_final: 0.4908 (m-80) REVERT: C 213 LYS cc_start: 0.7587 (tptm) cc_final: 0.6868 (ttmt) REVERT: C 255 MET cc_start: 0.7465 (tpt) cc_final: 0.6835 (mmt) REVERT: C 305 LYS cc_start: 0.8622 (tptt) cc_final: 0.8296 (tptt) REVERT: E 38 LEU cc_start: 0.8588 (mt) cc_final: 0.8101 (tp) REVERT: E 42 LEU cc_start: 0.8854 (mt) cc_final: 0.8464 (mt) REVERT: E 83 ASP cc_start: 0.7613 (m-30) cc_final: 0.7027 (t70) REVERT: E 153 MET cc_start: 0.8490 (mtp) cc_final: 0.7948 (ttm) REVERT: E 240 THR cc_start: 0.9429 (OUTLIER) cc_final: 0.9061 (p) REVERT: E 249 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7208 (tp30) REVERT: E 414 ASN cc_start: 0.8200 (t0) cc_final: 0.7831 (t0) REVERT: E 495 ASP cc_start: 0.7451 (t0) cc_final: 0.7102 (t0) REVERT: E 592 ASP cc_start: 0.7764 (t0) cc_final: 0.7450 (p0) REVERT: E 1683 LEU cc_start: 0.8987 (tp) cc_final: 0.8720 (pp) REVERT: G 6 ASN cc_start: 0.8383 (p0) cc_final: 0.8108 (m-40) REVERT: G 90 LEU cc_start: 0.6736 (tp) cc_final: 0.5920 (tt) REVERT: I 329 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7535 (ttpp) REVERT: I 331 PHE cc_start: 0.7183 (m-10) cc_final: 0.6754 (m-10) REVERT: I 366 MET cc_start: 0.7454 (tpt) cc_final: 0.7094 (tpp) REVERT: I 391 LEU cc_start: 0.9383 (mt) cc_final: 0.9156 (tp) REVERT: J 326 TYR cc_start: 0.6937 (p90) cc_final: 0.6277 (p90) REVERT: J 333 ILE cc_start: 0.6870 (tp) cc_final: 0.6119 (tp) REVERT: J 375 VAL cc_start: 0.7578 (p) cc_final: 0.7306 (m) outliers start: 58 outliers final: 13 residues processed: 1549 average time/residue: 0.5917 time to fit residues: 1497.8847 Evaluate side-chains 798 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 780 time to evaluate : 5.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1664 THR Chi-restraints excluded: chain J residue 309 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 641 optimal weight: 1.9990 chunk 576 optimal weight: 3.9990 chunk 319 optimal weight: 0.9990 chunk 196 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 307 optimal weight: 0.9980 chunk 595 optimal weight: 0.5980 chunk 230 optimal weight: 7.9990 chunk 362 optimal weight: 3.9990 chunk 443 optimal weight: 0.0040 chunk 690 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 HIS B 967 HIS B 992 GLN B1084 HIS B1157 HIS B1205 ASN B1207 GLN B1308 GLN B1355 GLN B1439 HIS B1509 GLN B1561 GLN B1693 HIS B1726 GLN B1741 GLN B1791 HIS B1915 HIS ** B1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2106 HIS B2319 ASN D 28 GLN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 HIS ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN ** F 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN H 88 GLN A 743 HIS A 763 ASN ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 HIS A1308 GLN A1355 GLN A1729 GLN A1765 ASN A2106 HIS C 30 HIS ** C 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 ASN E 496 HIS E 540 HIS ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 832 HIS ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN I 390 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 59658 Z= 0.197 Angle : 0.597 15.715 80992 Z= 0.309 Chirality : 0.041 0.204 9400 Planarity : 0.004 0.055 10390 Dihedral : 4.042 55.163 8295 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.54 % Favored : 96.40 % Rotamer: Outliers : 2.50 % Allowed : 10.61 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 7536 helix: 1.02 (0.08), residues: 4660 sheet: -0.14 (0.28), residues: 350 loop : -1.00 (0.13), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 99 HIS 0.020 0.001 HIS A2189 PHE 0.031 0.001 PHE F1531 TYR 0.026 0.001 TYR E 731 ARG 0.007 0.001 ARG H 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 899 time to evaluate : 5.284 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: B 655 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7866 (p) REVERT: B 772 MET cc_start: 0.8556 (mmp) cc_final: 0.8269 (mmm) REVERT: B 1227 GLU cc_start: 0.8035 (tp30) cc_final: 0.7750 (tt0) REVERT: B 1285 ARG cc_start: 0.7340 (ptm-80) cc_final: 0.7044 (ttp80) REVERT: B 1539 ASP cc_start: 0.7909 (t0) cc_final: 0.7491 (t0) REVERT: B 1960 LEU cc_start: 0.8955 (pp) cc_final: 0.8594 (tp) REVERT: B 2047 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7289 (ttp) REVERT: B 2102 ASP cc_start: 0.7906 (t0) cc_final: 0.7698 (t0) REVERT: B 2135 ASP cc_start: 0.8214 (t0) cc_final: 0.7966 (t0) REVERT: B 2175 MET cc_start: 0.8504 (tpp) cc_final: 0.8280 (mmm) REVERT: B 2274 ASP cc_start: 0.7412 (p0) cc_final: 0.7187 (p0) REVERT: B 2357 ASP cc_start: 0.8215 (t0) cc_final: 0.7892 (t0) REVERT: D 62 TYR cc_start: 0.7666 (t80) cc_final: 0.7376 (t80) REVERT: D 69 ASP cc_start: 0.7975 (t0) cc_final: 0.7717 (p0) REVERT: D 114 LEU cc_start: 0.7017 (tp) cc_final: 0.6723 (tp) REVERT: D 137 HIS cc_start: 0.6031 (t70) cc_final: 0.5585 (t70) REVERT: D 213 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7759 (mtpt) REVERT: D 225 GLN cc_start: 0.7444 (tt0) cc_final: 0.7208 (tm-30) REVERT: F 76 LYS cc_start: 0.8273 (mttp) cc_final: 0.8056 (mtmm) REVERT: F 111 ILE cc_start: 0.8252 (mt) cc_final: 0.8036 (tp) REVERT: F 251 GLU cc_start: 0.8021 (mp0) cc_final: 0.7789 (mp0) REVERT: F 433 MET cc_start: 0.8251 (ttm) cc_final: 0.8043 (ttm) REVERT: F 482 MET cc_start: 0.8487 (ttp) cc_final: 0.8167 (ttm) REVERT: F 953 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8765 (mp) REVERT: F 1529 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6587 (tt) REVERT: F 1633 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7084 (mp0) REVERT: H 94 ARG cc_start: 0.7937 (ttm110) cc_final: 0.7618 (ttm170) REVERT: A 617 GLU cc_start: 0.6842 (tm-30) cc_final: 0.6451 (mt-10) REVERT: A 668 ASP cc_start: 0.7359 (p0) cc_final: 0.7050 (p0) REVERT: A 796 ASN cc_start: 0.8077 (m-40) cc_final: 0.7832 (m-40) REVERT: A 1269 TRP cc_start: 0.7484 (m100) cc_final: 0.6743 (m-10) REVERT: A 1503 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7690 (pp) REVERT: A 1724 MET cc_start: 0.9097 (mmp) cc_final: 0.8420 (tpp) REVERT: A 2514 SER cc_start: 0.7336 (t) cc_final: 0.7109 (p) REVERT: C 41 GLN cc_start: 0.8034 (tp40) cc_final: 0.7821 (pm20) REVERT: C 213 LYS cc_start: 0.7543 (tptm) cc_final: 0.7023 (ttmt) REVERT: C 255 MET cc_start: 0.7582 (tpt) cc_final: 0.6961 (mmt) REVERT: C 273 MET cc_start: 0.7781 (ttp) cc_final: 0.7489 (ttp) REVERT: E 38 LEU cc_start: 0.8694 (mt) cc_final: 0.8447 (tp) REVERT: E 42 LEU cc_start: 0.8799 (mt) cc_final: 0.8498 (mt) REVERT: E 55 ARG cc_start: 0.7021 (mmm160) cc_final: 0.6727 (tpp-160) REVERT: E 83 ASP cc_start: 0.7653 (m-30) cc_final: 0.7093 (t70) REVERT: E 136 GLN cc_start: 0.7211 (tp40) cc_final: 0.6984 (tp40) REVERT: E 153 MET cc_start: 0.8457 (mtp) cc_final: 0.8118 (ttm) REVERT: E 213 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7572 (tttm) REVERT: E 240 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9088 (p) REVERT: E 249 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7217 (mm-30) REVERT: E 414 ASN cc_start: 0.8209 (t0) cc_final: 0.7576 (t0) REVERT: E 529 LEU cc_start: 0.8106 (mt) cc_final: 0.7222 (pp) REVERT: E 592 ASP cc_start: 0.7587 (t0) cc_final: 0.7355 (p0) REVERT: E 831 TRP cc_start: 0.7583 (m100) cc_final: 0.7216 (m100) REVERT: G 6 ASN cc_start: 0.8421 (p0) cc_final: 0.8118 (m-40) REVERT: I 319 LEU cc_start: 0.7900 (tt) cc_final: 0.7247 (tp) REVERT: I 329 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7441 (ttpp) REVERT: I 331 PHE cc_start: 0.6856 (m-10) cc_final: 0.6297 (m-10) REVERT: I 391 LEU cc_start: 0.9373 (mt) cc_final: 0.9165 (tp) REVERT: J 353 GLN cc_start: 0.7832 (tp40) cc_final: 0.7593 (tp40) outliers start: 148 outliers final: 79 residues processed: 1006 average time/residue: 0.5635 time to fit residues: 962.0985 Evaluate side-chains 776 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 690 time to evaluate : 5.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1287 LEU Chi-restraints excluded: chain B residue 1293 LYS Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1542 ASP Chi-restraints excluded: chain B residue 1607 LEU Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 2021 ILE Chi-restraints excluded: chain B residue 2047 MET Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain F residue 495 ASP Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 712 LEU Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1529 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 686 HIS Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1476 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1558 SER Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2307 SER Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2387 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1664 THR Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain I residue 384 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 383 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 574 optimal weight: 2.9990 chunk 469 optimal weight: 0.4980 chunk 190 optimal weight: 0.5980 chunk 691 optimal weight: 3.9990 chunk 746 optimal weight: 8.9990 chunk 615 optimal weight: 6.9990 chunk 685 optimal weight: 0.8980 chunk 235 optimal weight: 5.9990 chunk 554 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 HIS ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 HIS F 59 HIS ** F 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 758 GLN ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 932 ASN F1645 GLN A 967 HIS A1562 GLN C 30 HIS ** C 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN E 889 HIS ** E1485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1632 HIS I 390 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 59658 Z= 0.194 Angle : 0.550 13.833 80992 Z= 0.280 Chirality : 0.040 0.210 9400 Planarity : 0.004 0.050 10390 Dihedral : 3.982 59.205 8286 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.30 % Rotamer: Outliers : 2.56 % Allowed : 12.20 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.10), residues: 7536 helix: 1.15 (0.08), residues: 4740 sheet: -0.27 (0.28), residues: 356 loop : -1.05 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2429 HIS 0.021 0.001 HIS E 72 PHE 0.033 0.001 PHE F1531 TYR 0.021 0.001 TYR A1209 ARG 0.010 0.000 ARG G 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 751 time to evaluate : 5.200 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: B 772 MET cc_start: 0.8509 (mmp) cc_final: 0.8239 (mmm) REVERT: B 821 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8124 (t80) REVERT: B 1018 MET cc_start: 0.8503 (mmt) cc_final: 0.8038 (mpp) REVERT: B 1227 GLU cc_start: 0.8083 (tp30) cc_final: 0.7801 (tt0) REVERT: B 1285 ARG cc_start: 0.7370 (ptm-80) cc_final: 0.7052 (ttp80) REVERT: B 1477 MET cc_start: 0.8410 (ppp) cc_final: 0.8014 (ppp) REVERT: B 1539 ASP cc_start: 0.7928 (t0) cc_final: 0.7486 (t0) REVERT: B 1960 LEU cc_start: 0.8869 (pp) cc_final: 0.8614 (tp) REVERT: B 2135 ASP cc_start: 0.8206 (t0) cc_final: 0.7929 (t0) REVERT: B 2175 MET cc_start: 0.8525 (tpp) cc_final: 0.8280 (mmm) REVERT: B 2274 ASP cc_start: 0.7600 (p0) cc_final: 0.7282 (p0) REVERT: B 2281 MET cc_start: 0.7839 (tpp) cc_final: 0.7569 (tpp) REVERT: B 2357 ASP cc_start: 0.8283 (t0) cc_final: 0.7894 (t0) REVERT: D 137 HIS cc_start: 0.6355 (t70) cc_final: 0.5725 (t70) REVERT: D 246 ILE cc_start: 0.8592 (mt) cc_final: 0.8304 (mm) REVERT: D 297 TRP cc_start: 0.8016 (m100) cc_final: 0.7737 (m-10) REVERT: F 433 MET cc_start: 0.8267 (ttm) cc_final: 0.8013 (ttm) REVERT: F 495 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8402 (m-30) REVERT: F 594 ASP cc_start: 0.8185 (m-30) cc_final: 0.7540 (t0) REVERT: F 953 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8738 (mp) REVERT: F 1633 GLU cc_start: 0.7716 (mt-10) cc_final: 0.6967 (mp0) REVERT: H 94 ARG cc_start: 0.7866 (ttm110) cc_final: 0.7624 (ttm170) REVERT: A 617 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6505 (mt-10) REVERT: A 668 ASP cc_start: 0.7297 (p0) cc_final: 0.7013 (p0) REVERT: A 796 ASN cc_start: 0.8030 (m-40) cc_final: 0.7783 (m-40) REVERT: A 1044 MET cc_start: 0.7205 (mmp) cc_final: 0.6866 (mmm) REVERT: A 1269 TRP cc_start: 0.7411 (m100) cc_final: 0.6739 (m-10) REVERT: A 1289 LEU cc_start: 0.8503 (mm) cc_final: 0.8269 (mt) REVERT: A 1503 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7809 (pp) REVERT: A 1798 PHE cc_start: 0.9127 (t80) cc_final: 0.8639 (t80) REVERT: A 1904 LEU cc_start: 0.8818 (tp) cc_final: 0.8540 (mt) REVERT: A 2175 MET cc_start: 0.8231 (mmm) cc_final: 0.7987 (tpp) REVERT: A 2387 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7844 (mtm) REVERT: C 41 GLN cc_start: 0.8097 (tp40) cc_final: 0.7882 (pm20) REVERT: C 213 LYS cc_start: 0.7497 (tptm) cc_final: 0.6938 (ttmt) REVERT: C 255 MET cc_start: 0.7508 (tpt) cc_final: 0.6817 (mmt) REVERT: C 273 MET cc_start: 0.7789 (ttp) cc_final: 0.7473 (ttp) REVERT: E 42 LEU cc_start: 0.8712 (mt) cc_final: 0.8508 (mt) REVERT: E 55 ARG cc_start: 0.7023 (mmm160) cc_final: 0.6777 (tpp-160) REVERT: E 72 HIS cc_start: 0.7005 (p-80) cc_final: 0.6799 (p90) REVERT: E 83 ASP cc_start: 0.7822 (m-30) cc_final: 0.7339 (t70) REVERT: E 136 GLN cc_start: 0.7245 (tp40) cc_final: 0.6974 (tp40) REVERT: E 153 MET cc_start: 0.8429 (mtp) cc_final: 0.8190 (ttm) REVERT: E 213 LYS cc_start: 0.8242 (mtmt) cc_final: 0.7613 (tttm) REVERT: E 249 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7109 (mm-30) REVERT: E 414 ASN cc_start: 0.8223 (t0) cc_final: 0.7833 (t0) REVERT: E 529 LEU cc_start: 0.8177 (mt) cc_final: 0.7292 (pp) REVERT: E 625 ASP cc_start: 0.8434 (t0) cc_final: 0.8202 (t0) REVERT: E 678 LYS cc_start: 0.9068 (mmmt) cc_final: 0.8114 (ttpt) REVERT: E 831 TRP cc_start: 0.7576 (m100) cc_final: 0.7249 (m100) REVERT: E 1522 TYR cc_start: 0.5635 (t80) cc_final: 0.5432 (t80) REVERT: G 92 ARG cc_start: 0.8553 (ttm110) cc_final: 0.8259 (ttp-110) REVERT: G 105 ASN cc_start: 0.8970 (m-40) cc_final: 0.8725 (p0) REVERT: I 329 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7496 (ttpp) REVERT: I 331 PHE cc_start: 0.6795 (m-10) cc_final: 0.6275 (m-10) REVERT: I 391 LEU cc_start: 0.9370 (mt) cc_final: 0.9162 (tp) REVERT: I 401 MET cc_start: 0.7743 (ttm) cc_final: 0.7503 (mmm) REVERT: J 366 MET cc_start: 0.7354 (tpp) cc_final: 0.7038 (tpp) REVERT: J 404 MET cc_start: 0.7420 (ttp) cc_final: 0.6930 (tmm) outliers start: 152 outliers final: 85 residues processed: 859 average time/residue: 0.5450 time to fit residues: 801.1027 Evaluate side-chains 761 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 671 time to evaluate : 5.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1541 HIS Chi-restraints excluded: chain B residue 1607 LEU Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 2150 ILE Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2349 LEU Chi-restraints excluded: chain B residue 2414 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 495 ASP Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 689 CYS Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1621 ILE Chi-restraints excluded: chain F residue 1634 THR Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 686 HIS Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1437 MET Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2172 LEU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2387 MET Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 935 SER Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1664 THR Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain I residue 384 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Chi-restraints excluded: chain J residue 400 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 683 optimal weight: 6.9990 chunk 519 optimal weight: 2.9990 chunk 358 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 329 optimal weight: 1.9990 chunk 464 optimal weight: 4.9990 chunk 693 optimal weight: 0.9990 chunk 734 optimal weight: 8.9990 chunk 362 optimal weight: 1.9990 chunk 657 optimal weight: 0.6980 chunk 197 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 HIS B2189 HIS ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS F 569 GLN ** F 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN C 30 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 435 ASN ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN E 783 ASN E1485 GLN I 390 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 59658 Z= 0.164 Angle : 0.530 11.202 80992 Z= 0.267 Chirality : 0.039 0.270 9400 Planarity : 0.003 0.052 10390 Dihedral : 3.917 55.451 8284 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Rotamer: Outliers : 2.67 % Allowed : 13.24 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.10), residues: 7536 helix: 1.28 (0.08), residues: 4768 sheet: -0.29 (0.28), residues: 364 loop : -1.05 (0.13), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B1757 HIS 0.009 0.001 HIS A2189 PHE 0.026 0.001 PHE B1322 TYR 0.024 0.001 TYR C 101 ARG 0.007 0.000 ARG A2086 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 720 time to evaluate : 5.328 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: symmetry clash REVERT: B 772 MET cc_start: 0.8543 (mmp) cc_final: 0.8268 (mmm) REVERT: B 821 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8182 (t80) REVERT: B 1018 MET cc_start: 0.8456 (mmt) cc_final: 0.8025 (mpp) REVERT: B 1285 ARG cc_start: 0.7418 (ptm-80) cc_final: 0.7024 (mtp-110) REVERT: B 1477 MET cc_start: 0.8340 (ppp) cc_final: 0.7842 (ppp) REVERT: B 1539 ASP cc_start: 0.7962 (t0) cc_final: 0.7542 (t0) REVERT: B 1955 ARG cc_start: 0.7829 (ptm160) cc_final: 0.7497 (ptm-80) REVERT: B 1960 LEU cc_start: 0.8887 (pp) cc_final: 0.8437 (tp) REVERT: B 1963 ASP cc_start: 0.7890 (m-30) cc_final: 0.7682 (m-30) REVERT: B 2079 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6902 (mtm) REVERT: B 2135 ASP cc_start: 0.8156 (t0) cc_final: 0.7920 (t0) REVERT: B 2175 MET cc_start: 0.8504 (tpp) cc_final: 0.8255 (mmm) REVERT: B 2189 HIS cc_start: 0.6605 (OUTLIER) cc_final: 0.6239 (t70) REVERT: B 2281 MET cc_start: 0.7755 (tpp) cc_final: 0.7515 (tpp) REVERT: B 2357 ASP cc_start: 0.8332 (t0) cc_final: 0.7947 (t0) REVERT: D 137 HIS cc_start: 0.6704 (t70) cc_final: 0.6045 (t70) REVERT: D 273 MET cc_start: 0.8628 (tpp) cc_final: 0.8390 (tpt) REVERT: F 495 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8351 (m-30) REVERT: F 594 ASP cc_start: 0.8200 (m-30) cc_final: 0.7556 (t0) REVERT: H 24 THR cc_start: 0.8688 (m) cc_final: 0.8453 (m) REVERT: H 94 ARG cc_start: 0.7859 (ttm110) cc_final: 0.7578 (ttm170) REVERT: A 654 ASP cc_start: 0.7977 (t0) cc_final: 0.7776 (t0) REVERT: A 796 ASN cc_start: 0.8111 (m-40) cc_final: 0.7905 (m-40) REVERT: A 813 MET cc_start: 0.8674 (ptm) cc_final: 0.8467 (ptm) REVERT: A 1269 TRP cc_start: 0.7442 (m100) cc_final: 0.6725 (m-10) REVERT: A 1289 LEU cc_start: 0.8468 (mm) cc_final: 0.8253 (mt) REVERT: A 1503 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7909 (pp) REVERT: A 1539 ASP cc_start: 0.7991 (t0) cc_final: 0.7704 (t0) REVERT: A 1873 LEU cc_start: 0.6854 (tt) cc_final: 0.6458 (tp) REVERT: A 1904 LEU cc_start: 0.8783 (tp) cc_final: 0.8551 (mt) REVERT: A 2175 MET cc_start: 0.8255 (mmm) cc_final: 0.7998 (tpp) REVERT: A 2297 ASP cc_start: 0.8483 (p0) cc_final: 0.8182 (p0) REVERT: A 2387 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7900 (mtm) REVERT: C 213 LYS cc_start: 0.7527 (tptm) cc_final: 0.6989 (ttmt) REVERT: C 255 MET cc_start: 0.7623 (tpt) cc_final: 0.6892 (mmt) REVERT: E 55 ARG cc_start: 0.7002 (mmm160) cc_final: 0.6750 (tpp-160) REVERT: E 83 ASP cc_start: 0.7836 (m-30) cc_final: 0.7344 (t70) REVERT: E 136 GLN cc_start: 0.7240 (tp40) cc_final: 0.6994 (tp40) REVERT: E 153 MET cc_start: 0.8418 (mtp) cc_final: 0.8201 (ttm) REVERT: E 213 LYS cc_start: 0.8242 (mtmt) cc_final: 0.7579 (tttm) REVERT: E 240 THR cc_start: 0.9357 (OUTLIER) cc_final: 0.9077 (p) REVERT: E 249 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7099 (mm-30) REVERT: E 366 ASP cc_start: 0.7748 (m-30) cc_final: 0.7176 (t0) REVERT: E 414 ASN cc_start: 0.8173 (t0) cc_final: 0.7773 (t0) REVERT: E 529 LEU cc_start: 0.8112 (mt) cc_final: 0.7237 (pp) REVERT: E 591 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7446 (mt) REVERT: E 625 ASP cc_start: 0.8423 (t0) cc_final: 0.8199 (t0) REVERT: E 678 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8275 (ttpt) REVERT: E 790 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.6734 (mpp) REVERT: E 831 TRP cc_start: 0.7543 (m100) cc_final: 0.7249 (m100) REVERT: E 946 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6302 (pt0) REVERT: G 103 CYS cc_start: 0.7535 (t) cc_final: 0.6730 (t) REVERT: I 329 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7694 (ttpp) REVERT: I 331 PHE cc_start: 0.6681 (m-10) cc_final: 0.6117 (m-10) REVERT: J 366 MET cc_start: 0.7250 (tpp) cc_final: 0.7000 (tpp) REVERT: J 404 MET cc_start: 0.7239 (ttp) cc_final: 0.6740 (ppp) outliers start: 158 outliers final: 99 residues processed: 825 average time/residue: 0.5522 time to fit residues: 784.6593 Evaluate side-chains 772 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 663 time to evaluate : 5.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1541 HIS Chi-restraints excluded: chain B residue 1542 ASP Chi-restraints excluded: chain B residue 1607 LEU Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 2079 MET Chi-restraints excluded: chain B residue 2150 ILE Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2189 HIS Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 495 ASP Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 689 CYS Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1621 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1437 MET Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1515 MET Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1590 MET Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2172 LEU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2307 SER Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2387 MET Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 790 MET Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 935 SER Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 946 GLU Chi-restraints excluded: chain E residue 1607 MET Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain I residue 384 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Chi-restraints excluded: chain J residue 400 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 611 optimal weight: 0.5980 chunk 417 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 546 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 626 optimal weight: 2.9990 chunk 507 optimal weight: 0.0170 chunk 0 optimal weight: 50.0000 chunk 375 optimal weight: 10.0000 chunk 659 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 HIS B 752 GLN B2028 HIS B2189 HIS D 64 HIS ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 687 ASN ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 988 HIS F1632 HIS A 763 ASN A1084 HIS A2428 ASN C 30 HIS C 311 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 785 HIS ** E1485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 59658 Z= 0.188 Angle : 0.536 10.998 80992 Z= 0.269 Chirality : 0.040 0.245 9400 Planarity : 0.003 0.053 10390 Dihedral : 3.907 52.883 8282 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Rotamer: Outliers : 3.00 % Allowed : 14.02 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.10), residues: 7536 helix: 1.40 (0.08), residues: 4746 sheet: -0.22 (0.27), residues: 374 loop : -1.03 (0.13), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A2429 HIS 0.026 0.001 HIS B2189 PHE 0.025 0.001 PHE E 63 TYR 0.024 0.001 TYR D 68 ARG 0.009 0.000 ARG I 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 706 time to evaluate : 5.316 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: B 821 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8181 (t80) REVERT: B 1285 ARG cc_start: 0.7469 (ptm-80) cc_final: 0.7036 (mtp-110) REVERT: B 1477 MET cc_start: 0.8286 (ppp) cc_final: 0.7859 (ppp) REVERT: B 1539 ASP cc_start: 0.7976 (t0) cc_final: 0.7508 (t0) REVERT: B 1724 MET cc_start: 0.8770 (mmm) cc_final: 0.8549 (tpp) REVERT: B 1960 LEU cc_start: 0.8789 (pp) cc_final: 0.8565 (tp) REVERT: B 2079 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6909 (mtm) REVERT: B 2089 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7630 (ttm) REVERT: B 2135 ASP cc_start: 0.8231 (t0) cc_final: 0.7957 (t0) REVERT: B 2175 MET cc_start: 0.8506 (tpp) cc_final: 0.8254 (mmm) REVERT: B 2233 ASN cc_start: 0.8518 (p0) cc_final: 0.8291 (p0) REVERT: B 2281 MET cc_start: 0.7804 (tpp) cc_final: 0.7585 (tpp) REVERT: B 2357 ASP cc_start: 0.8335 (t0) cc_final: 0.8000 (t0) REVERT: D 62 TYR cc_start: 0.7729 (t80) cc_final: 0.7428 (t80) REVERT: D 137 HIS cc_start: 0.6730 (t70) cc_final: 0.6331 (t70) REVERT: D 273 MET cc_start: 0.8595 (tpp) cc_final: 0.8281 (mmm) REVERT: F 594 ASP cc_start: 0.8224 (m-30) cc_final: 0.7594 (t0) REVERT: F 1633 GLU cc_start: 0.7746 (mt-10) cc_final: 0.6972 (mp0) REVERT: H 24 THR cc_start: 0.8620 (m) cc_final: 0.8391 (m) REVERT: H 36 VAL cc_start: 0.6004 (OUTLIER) cc_final: 0.5747 (p) REVERT: H 94 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7459 (ttm170) REVERT: A 613 SER cc_start: 0.7623 (p) cc_final: 0.7409 (m) REVERT: A 1044 MET cc_start: 0.7396 (mmp) cc_final: 0.7013 (mmm) REVERT: A 1269 TRP cc_start: 0.7463 (m100) cc_final: 0.6772 (m-10) REVERT: A 1289 LEU cc_start: 0.8493 (mm) cc_final: 0.8254 (mt) REVERT: A 1503 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7917 (pp) REVERT: A 1539 ASP cc_start: 0.8064 (t0) cc_final: 0.7767 (t0) REVERT: A 1798 PHE cc_start: 0.9047 (t80) cc_final: 0.8717 (t80) REVERT: A 1904 LEU cc_start: 0.8819 (tp) cc_final: 0.8605 (mt) REVERT: A 2161 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7189 (tm-30) REVERT: A 2175 MET cc_start: 0.8274 (mmm) cc_final: 0.8018 (tpp) REVERT: A 2297 ASP cc_start: 0.8557 (p0) cc_final: 0.8238 (p0) REVERT: C 213 LYS cc_start: 0.7333 (tptm) cc_final: 0.6821 (ttmt) REVERT: C 255 MET cc_start: 0.7639 (tpt) cc_final: 0.6867 (mmt) REVERT: C 273 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7599 (ttp) REVERT: E 55 ARG cc_start: 0.6969 (mmm160) cc_final: 0.6702 (tpp-160) REVERT: E 83 ASP cc_start: 0.7841 (m-30) cc_final: 0.7324 (t70) REVERT: E 136 GLN cc_start: 0.7288 (tp40) cc_final: 0.7050 (tp40) REVERT: E 213 LYS cc_start: 0.8275 (mtmt) cc_final: 0.7626 (tttm) REVERT: E 225 GLU cc_start: 0.7221 (mm-30) cc_final: 0.7011 (mt-10) REVERT: E 240 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.9098 (p) REVERT: E 249 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7153 (mm-30) REVERT: E 366 ASP cc_start: 0.7767 (m-30) cc_final: 0.7227 (t0) REVERT: E 414 ASN cc_start: 0.8263 (t0) cc_final: 0.7881 (t0) REVERT: E 528 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7260 (mp) REVERT: E 529 LEU cc_start: 0.8141 (mt) cc_final: 0.7221 (pp) REVERT: E 678 LYS cc_start: 0.9183 (mmmt) cc_final: 0.8383 (ttpt) REVERT: E 725 THR cc_start: 0.7344 (OUTLIER) cc_final: 0.7080 (p) REVERT: E 831 TRP cc_start: 0.7562 (m100) cc_final: 0.7282 (m100) REVERT: E 946 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.6203 (pt0) REVERT: E 1522 TYR cc_start: 0.5052 (t80) cc_final: 0.4682 (t80) REVERT: G 103 CYS cc_start: 0.7679 (t) cc_final: 0.6753 (t) REVERT: I 329 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7596 (ttpp) REVERT: I 331 PHE cc_start: 0.6656 (m-10) cc_final: 0.6157 (m-10) REVERT: I 386 ARG cc_start: 0.9175 (ttm110) cc_final: 0.8940 (mtp85) REVERT: I 391 LEU cc_start: 0.9217 (mt) cc_final: 0.8917 (tp) REVERT: I 401 MET cc_start: 0.7683 (mmm) cc_final: 0.7370 (mmm) REVERT: J 366 MET cc_start: 0.7241 (tpp) cc_final: 0.7002 (tpp) REVERT: J 404 MET cc_start: 0.7161 (ttp) cc_final: 0.6880 (tmm) outliers start: 178 outliers final: 111 residues processed: 828 average time/residue: 0.5643 time to fit residues: 801.3219 Evaluate side-chains 778 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 657 time to evaluate : 5.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1221 THR Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1338 ILE Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1541 HIS Chi-restraints excluded: chain B residue 1552 LEU Chi-restraints excluded: chain B residue 1607 LEU Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 1802 LEU Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2079 MET Chi-restraints excluded: chain B residue 2089 MET Chi-restraints excluded: chain B residue 2150 ILE Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2189 HIS Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2349 LEU Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 689 CYS Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1634 THR Chi-restraints excluded: chain F residue 1637 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1437 MET Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1515 MET Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2172 LEU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2307 SER Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 935 SER Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 946 GLU Chi-restraints excluded: chain E residue 978 THR Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain E residue 1693 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 247 optimal weight: 0.7980 chunk 661 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 431 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 735 optimal weight: 1.9990 chunk 610 optimal weight: 4.9990 chunk 340 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 386 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 HIS B2189 HIS ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 763 ASN A 796 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 311 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 569 GLN ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 671 HIS ** E 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1485 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 59658 Z= 0.188 Angle : 0.537 10.140 80992 Z= 0.269 Chirality : 0.040 0.208 9400 Planarity : 0.003 0.057 10390 Dihedral : 3.906 52.822 8282 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 2.80 % Allowed : 14.39 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.10), residues: 7536 helix: 1.46 (0.08), residues: 4742 sheet: -0.17 (0.27), residues: 364 loop : -1.06 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A2429 HIS 0.013 0.001 HIS B2189 PHE 0.017 0.001 PHE F1531 TYR 0.024 0.001 TYR B2542 ARG 0.007 0.000 ARG I 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 687 time to evaluate : 5.317 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: B 311 ARG cc_start: 0.7713 (ptm160) cc_final: 0.7425 (ptm160) REVERT: B 710 LEU cc_start: 0.7991 (tt) cc_final: 0.7737 (mt) REVERT: B 821 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8167 (t80) REVERT: B 1291 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8083 (mm) REVERT: B 1529 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.6869 (tmm) REVERT: B 1539 ASP cc_start: 0.8014 (t0) cc_final: 0.7616 (t0) REVERT: B 1565 ASP cc_start: 0.8064 (m-30) cc_final: 0.7477 (m-30) REVERT: B 1743 LEU cc_start: 0.8790 (tt) cc_final: 0.8132 (tp) REVERT: B 1747 MET cc_start: 0.8486 (mmm) cc_final: 0.7674 (mpp) REVERT: B 2079 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6860 (mtm) REVERT: B 2135 ASP cc_start: 0.8208 (t0) cc_final: 0.7890 (t0) REVERT: B 2175 MET cc_start: 0.8518 (tpp) cc_final: 0.8260 (mmm) REVERT: B 2233 ASN cc_start: 0.8632 (p0) cc_final: 0.8370 (p0) REVERT: B 2281 MET cc_start: 0.7822 (tpp) cc_final: 0.7590 (tpp) REVERT: B 2357 ASP cc_start: 0.8334 (t0) cc_final: 0.8073 (t0) REVERT: D 137 HIS cc_start: 0.6780 (t70) cc_final: 0.6478 (t70) REVERT: D 158 LYS cc_start: 0.5876 (tptt) cc_final: 0.5084 (mmmm) REVERT: D 245 LYS cc_start: 0.6866 (mmtt) cc_final: 0.6599 (mmtt) REVERT: D 273 MET cc_start: 0.8571 (tpp) cc_final: 0.8274 (mmm) REVERT: F 594 ASP cc_start: 0.8216 (m-30) cc_final: 0.7597 (t0) REVERT: F 1512 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.6054 (mp) REVERT: F 1633 GLU cc_start: 0.7768 (mt-10) cc_final: 0.6980 (mp0) REVERT: H 6 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8005 (m-40) REVERT: H 36 VAL cc_start: 0.6083 (OUTLIER) cc_final: 0.5819 (p) REVERT: H 94 ARG cc_start: 0.7930 (ttm110) cc_final: 0.7446 (ttm170) REVERT: A 1269 TRP cc_start: 0.7464 (m100) cc_final: 0.6786 (m-10) REVERT: A 1289 LEU cc_start: 0.8460 (mm) cc_final: 0.8203 (mt) REVERT: A 1313 MET cc_start: 0.8967 (tmm) cc_final: 0.7502 (tmm) REVERT: A 1458 ASP cc_start: 0.7648 (m-30) cc_final: 0.7343 (m-30) REVERT: A 1503 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7917 (pp) REVERT: A 1539 ASP cc_start: 0.8089 (t0) cc_final: 0.7744 (t0) REVERT: A 1798 PHE cc_start: 0.9019 (t80) cc_final: 0.8608 (t80) REVERT: A 1904 LEU cc_start: 0.8826 (tp) cc_final: 0.8614 (mt) REVERT: A 2161 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7139 (tm-30) REVERT: A 2175 MET cc_start: 0.8223 (mmm) cc_final: 0.7944 (tpp) REVERT: A 2297 ASP cc_start: 0.8570 (p0) cc_final: 0.8254 (p0) REVERT: C 213 LYS cc_start: 0.7340 (tptm) cc_final: 0.6827 (ttmt) REVERT: C 255 MET cc_start: 0.7723 (tpt) cc_final: 0.6900 (mmt) REVERT: E 55 ARG cc_start: 0.6970 (mmm160) cc_final: 0.6547 (tpp-160) REVERT: E 83 ASP cc_start: 0.7898 (m-30) cc_final: 0.7439 (t70) REVERT: E 136 GLN cc_start: 0.7344 (tp40) cc_final: 0.7106 (tp40) REVERT: E 213 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7644 (tttm) REVERT: E 225 GLU cc_start: 0.7255 (mm-30) cc_final: 0.7021 (mt-10) REVERT: E 240 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9097 (p) REVERT: E 249 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7220 (mm-30) REVERT: E 366 ASP cc_start: 0.7864 (m-30) cc_final: 0.7341 (t0) REVERT: E 414 ASN cc_start: 0.8283 (t0) cc_final: 0.7740 (t0) REVERT: E 453 MET cc_start: 0.8705 (tpp) cc_final: 0.8427 (mmt) REVERT: E 481 GLU cc_start: 0.8146 (mp0) cc_final: 0.7387 (mp0) REVERT: E 528 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7261 (mp) REVERT: E 529 LEU cc_start: 0.8158 (mt) cc_final: 0.7227 (pp) REVERT: E 671 HIS cc_start: 0.7149 (p-80) cc_final: 0.6818 (p90) REVERT: E 678 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8446 (ttpt) REVERT: E 725 THR cc_start: 0.7330 (OUTLIER) cc_final: 0.7066 (p) REVERT: E 831 TRP cc_start: 0.7594 (m100) cc_final: 0.7364 (m100) REVERT: E 946 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6193 (pt0) REVERT: G 8 THR cc_start: 0.8365 (m) cc_final: 0.8162 (p) REVERT: G 103 CYS cc_start: 0.7653 (t) cc_final: 0.6780 (t) REVERT: I 331 PHE cc_start: 0.6625 (m-10) cc_final: 0.6115 (m-10) REVERT: I 391 LEU cc_start: 0.9219 (mt) cc_final: 0.8920 (tp) REVERT: J 366 MET cc_start: 0.7290 (tpp) cc_final: 0.7014 (tpp) REVERT: J 404 MET cc_start: 0.7216 (ttp) cc_final: 0.7005 (tmm) outliers start: 166 outliers final: 111 residues processed: 803 average time/residue: 0.5428 time to fit residues: 748.0300 Evaluate side-chains 776 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 653 time to evaluate : 5.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1221 THR Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1338 ILE Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1529 MET Chi-restraints excluded: chain B residue 1541 HIS Chi-restraints excluded: chain B residue 1552 LEU Chi-restraints excluded: chain B residue 1607 LEU Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1802 LEU Chi-restraints excluded: chain B residue 2079 MET Chi-restraints excluded: chain B residue 2150 ILE Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2349 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1512 LEU Chi-restraints excluded: chain F residue 1634 THR Chi-restraints excluded: chain F residue 1637 LEU Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1437 MET Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1515 MET Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2172 LEU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2307 SER Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 935 SER Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 946 GLU Chi-restraints excluded: chain E residue 978 THR Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 708 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 418 optimal weight: 0.9980 chunk 536 optimal weight: 0.8980 chunk 416 optimal weight: 0.7980 chunk 618 optimal weight: 9.9990 chunk 410 optimal weight: 20.0000 chunk 732 optimal weight: 1.9990 chunk 458 optimal weight: 5.9990 chunk 446 optimal weight: 2.9990 chunk 338 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1554 GLN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 687 ASN ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1662 HIS A 763 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2537 ASN C 30 HIS ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 59658 Z= 0.176 Angle : 0.531 9.699 80992 Z= 0.266 Chirality : 0.039 0.190 9400 Planarity : 0.003 0.054 10390 Dihedral : 3.876 52.852 8282 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 2.78 % Allowed : 14.98 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.10), residues: 7536 helix: 1.52 (0.08), residues: 4742 sheet: -0.13 (0.27), residues: 374 loop : -1.06 (0.13), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A2429 HIS 0.007 0.001 HIS A2189 PHE 0.028 0.001 PHE E 63 TYR 0.013 0.001 TYR E 731 ARG 0.007 0.000 ARG F 380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 708 time to evaluate : 5.321 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: B 311 ARG cc_start: 0.7774 (ptm160) cc_final: 0.7468 (ptm160) REVERT: B 710 LEU cc_start: 0.7994 (tt) cc_final: 0.7751 (mt) REVERT: B 821 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8189 (t80) REVERT: B 1285 ARG cc_start: 0.7683 (ttt90) cc_final: 0.7343 (mtp-110) REVERT: B 1291 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8072 (mm) REVERT: B 1467 MET cc_start: 0.7505 (mtp) cc_final: 0.7304 (mtp) REVERT: B 1529 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.6883 (tmm) REVERT: B 1530 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7549 (mt-10) REVERT: B 1539 ASP cc_start: 0.8011 (t0) cc_final: 0.7609 (t0) REVERT: B 1565 ASP cc_start: 0.8074 (m-30) cc_final: 0.7388 (m-30) REVERT: B 1743 LEU cc_start: 0.8809 (tt) cc_final: 0.8184 (tp) REVERT: B 1747 MET cc_start: 0.8520 (mmm) cc_final: 0.7709 (mpp) REVERT: B 1904 LEU cc_start: 0.9131 (tp) cc_final: 0.8855 (tt) REVERT: B 2135 ASP cc_start: 0.8215 (t0) cc_final: 0.7996 (t0) REVERT: B 2175 MET cc_start: 0.8510 (tpp) cc_final: 0.8265 (mmm) REVERT: B 2233 ASN cc_start: 0.8689 (p0) cc_final: 0.8427 (p0) REVERT: B 2281 MET cc_start: 0.7821 (tpp) cc_final: 0.7615 (tpp) REVERT: B 2357 ASP cc_start: 0.8348 (t0) cc_final: 0.8084 (t0) REVERT: D 158 LYS cc_start: 0.6171 (tptt) cc_final: 0.5469 (mmmm) REVERT: D 245 LYS cc_start: 0.6827 (mmtt) cc_final: 0.6497 (mmtt) REVERT: D 255 MET cc_start: 0.8184 (mtp) cc_final: 0.7936 (mtp) REVERT: D 273 MET cc_start: 0.8633 (tpp) cc_final: 0.8315 (mmm) REVERT: F 594 ASP cc_start: 0.8206 (m-30) cc_final: 0.7608 (t0) REVERT: F 1512 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.6089 (mp) REVERT: F 1633 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7067 (mp0) REVERT: H 36 VAL cc_start: 0.6168 (OUTLIER) cc_final: 0.5913 (p) REVERT: H 94 ARG cc_start: 0.7853 (ttm110) cc_final: 0.7329 (ttm170) REVERT: A 1289 LEU cc_start: 0.8471 (mm) cc_final: 0.8189 (mt) REVERT: A 1313 MET cc_start: 0.8963 (tmm) cc_final: 0.7929 (tpp) REVERT: A 1458 ASP cc_start: 0.7580 (m-30) cc_final: 0.7289 (m-30) REVERT: A 1503 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7962 (pp) REVERT: A 1539 ASP cc_start: 0.8093 (t0) cc_final: 0.7747 (t0) REVERT: A 2161 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7085 (tm-30) REVERT: A 2175 MET cc_start: 0.8255 (mmm) cc_final: 0.7987 (tpp) REVERT: A 2297 ASP cc_start: 0.8583 (p0) cc_final: 0.8163 (p0) REVERT: A 2387 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.8024 (mtm) REVERT: C 51 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7132 (p) REVERT: C 213 LYS cc_start: 0.7488 (tptm) cc_final: 0.7023 (ttmt) REVERT: C 255 MET cc_start: 0.7753 (tpt) cc_final: 0.6887 (mmt) REVERT: E 55 ARG cc_start: 0.6985 (mmm160) cc_final: 0.6567 (tpp-160) REVERT: E 83 ASP cc_start: 0.7788 (m-30) cc_final: 0.7351 (t70) REVERT: E 213 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7663 (tttm) REVERT: E 225 GLU cc_start: 0.7254 (mm-30) cc_final: 0.7025 (mt-10) REVERT: E 240 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9095 (p) REVERT: E 249 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7223 (mm-30) REVERT: E 366 ASP cc_start: 0.7836 (m-30) cc_final: 0.7288 (t0) REVERT: E 414 ASN cc_start: 0.8262 (t0) cc_final: 0.7897 (t0) REVERT: E 481 GLU cc_start: 0.8134 (mp0) cc_final: 0.7394 (mp0) REVERT: E 528 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7239 (mp) REVERT: E 529 LEU cc_start: 0.8159 (mt) cc_final: 0.7223 (pp) REVERT: E 663 ILE cc_start: 0.8033 (pt) cc_final: 0.7789 (mt) REVERT: E 671 HIS cc_start: 0.7333 (p-80) cc_final: 0.6887 (p90) REVERT: E 678 LYS cc_start: 0.9209 (mmmt) cc_final: 0.8464 (ttpt) REVERT: E 725 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.7082 (p) REVERT: E 790 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7110 (mpp) REVERT: E 831 TRP cc_start: 0.7642 (m100) cc_final: 0.7410 (m100) REVERT: E 946 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6208 (pt0) REVERT: G 8 THR cc_start: 0.8394 (m) cc_final: 0.8186 (p) REVERT: G 103 CYS cc_start: 0.7686 (t) cc_final: 0.6877 (t) REVERT: I 331 PHE cc_start: 0.6780 (m-10) cc_final: 0.6116 (m-10) REVERT: I 391 LEU cc_start: 0.9212 (mt) cc_final: 0.8933 (tp) REVERT: J 353 GLN cc_start: 0.8138 (tp40) cc_final: 0.7869 (tp40) REVERT: J 366 MET cc_start: 0.7202 (tpp) cc_final: 0.6895 (tpp) REVERT: J 404 MET cc_start: 0.7189 (ttp) cc_final: 0.6743 (ppp) outliers start: 165 outliers final: 116 residues processed: 821 average time/residue: 0.5467 time to fit residues: 774.4851 Evaluate side-chains 781 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 652 time to evaluate : 5.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1221 THR Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1338 ILE Chi-restraints excluded: chain B residue 1380 ILE Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1529 MET Chi-restraints excluded: chain B residue 1541 HIS Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1802 LEU Chi-restraints excluded: chain B residue 2148 GLN Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2349 LEU Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1512 LEU Chi-restraints excluded: chain F residue 1611 LEU Chi-restraints excluded: chain F residue 1634 THR Chi-restraints excluded: chain F residue 1637 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1515 MET Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2172 LEU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2307 SER Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2387 MET Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2548 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 790 MET Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 935 SER Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 946 GLU Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1664 THR Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain I residue 384 ASP Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 453 optimal weight: 0.7980 chunk 292 optimal weight: 3.9990 chunk 437 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 465 optimal weight: 0.0050 chunk 499 optimal weight: 1.9990 chunk 362 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 575 optimal weight: 2.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 743 HIS ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN F 43 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 59658 Z= 0.173 Angle : 0.540 17.234 80992 Z= 0.269 Chirality : 0.040 0.248 9400 Planarity : 0.004 0.057 10390 Dihedral : 3.851 52.980 8281 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 2.61 % Allowed : 15.49 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.10), residues: 7536 helix: 1.57 (0.08), residues: 4752 sheet: -0.24 (0.27), residues: 368 loop : -1.02 (0.13), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A2429 HIS 0.016 0.001 HIS B2189 PHE 0.014 0.001 PHE B1122 TYR 0.025 0.001 TYR B2542 ARG 0.012 0.000 ARG I 386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 686 time to evaluate : 5.219 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: B 304 MET cc_start: 0.5810 (tmm) cc_final: 0.5236 (tmm) REVERT: B 311 ARG cc_start: 0.7817 (ptm160) cc_final: 0.7496 (ptm160) REVERT: B 821 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8195 (t80) REVERT: B 1291 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8094 (mm) REVERT: B 1529 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.6897 (tmm) REVERT: B 1530 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7508 (mt-10) REVERT: B 1539 ASP cc_start: 0.8008 (t0) cc_final: 0.7585 (t0) REVERT: B 1565 ASP cc_start: 0.8078 (m-30) cc_final: 0.7383 (m-30) REVERT: B 1743 LEU cc_start: 0.8813 (tt) cc_final: 0.8178 (tp) REVERT: B 1747 MET cc_start: 0.8507 (mmm) cc_final: 0.7690 (mpp) REVERT: B 1904 LEU cc_start: 0.9127 (tp) cc_final: 0.8846 (tt) REVERT: B 2135 ASP cc_start: 0.8474 (t0) cc_final: 0.8229 (t0) REVERT: B 2175 MET cc_start: 0.8524 (tpp) cc_final: 0.8273 (mmm) REVERT: B 2233 ASN cc_start: 0.8719 (p0) cc_final: 0.8439 (p0) REVERT: B 2281 MET cc_start: 0.7837 (tpp) cc_final: 0.7609 (tpp) REVERT: D 158 LYS cc_start: 0.6133 (tptt) cc_final: 0.5458 (mmmm) REVERT: D 245 LYS cc_start: 0.6884 (mmtt) cc_final: 0.6540 (mmtt) REVERT: D 273 MET cc_start: 0.8586 (tpp) cc_final: 0.8293 (mmm) REVERT: F 594 ASP cc_start: 0.8196 (m-30) cc_final: 0.7622 (t0) REVERT: F 716 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8231 (mp) REVERT: F 1512 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6157 (mp) REVERT: F 1532 GLN cc_start: 0.7481 (tp40) cc_final: 0.7225 (pp30) REVERT: H 36 VAL cc_start: 0.6193 (OUTLIER) cc_final: 0.5960 (p) REVERT: H 94 ARG cc_start: 0.7846 (ttm110) cc_final: 0.7323 (ttm170) REVERT: A 1289 LEU cc_start: 0.8506 (mm) cc_final: 0.8232 (mt) REVERT: A 1313 MET cc_start: 0.8970 (tmm) cc_final: 0.8557 (tpp) REVERT: A 1458 ASP cc_start: 0.7588 (m-30) cc_final: 0.7270 (m-30) REVERT: A 1503 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8020 (pp) REVERT: A 1539 ASP cc_start: 0.8140 (t0) cc_final: 0.7806 (t0) REVERT: A 2089 MET cc_start: 0.7928 (mpp) cc_final: 0.7512 (mpp) REVERT: A 2161 GLN cc_start: 0.7599 (tm-30) cc_final: 0.7073 (tm-30) REVERT: A 2175 MET cc_start: 0.8258 (mmm) cc_final: 0.7984 (tpp) REVERT: A 2297 ASP cc_start: 0.8593 (p0) cc_final: 0.8167 (p0) REVERT: C 213 LYS cc_start: 0.7470 (tptm) cc_final: 0.7016 (ttmt) REVERT: C 255 MET cc_start: 0.7803 (tpt) cc_final: 0.6924 (mmt) REVERT: E 55 ARG cc_start: 0.7006 (mmm160) cc_final: 0.6575 (tpp-160) REVERT: E 83 ASP cc_start: 0.7921 (m-30) cc_final: 0.7492 (t70) REVERT: E 213 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7671 (tttm) REVERT: E 225 GLU cc_start: 0.7243 (mm-30) cc_final: 0.7017 (mt-10) REVERT: E 240 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.9091 (p) REVERT: E 249 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7232 (mm-30) REVERT: E 366 ASP cc_start: 0.7854 (m-30) cc_final: 0.7333 (t0) REVERT: E 414 ASN cc_start: 0.8268 (t0) cc_final: 0.7918 (t0) REVERT: E 481 GLU cc_start: 0.8137 (mp0) cc_final: 0.7399 (mp0) REVERT: E 528 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7278 (mp) REVERT: E 529 LEU cc_start: 0.8171 (mt) cc_final: 0.7239 (pp) REVERT: E 663 ILE cc_start: 0.8114 (pt) cc_final: 0.7847 (mt) REVERT: E 671 HIS cc_start: 0.7230 (p-80) cc_final: 0.6758 (p90) REVERT: E 725 THR cc_start: 0.7323 (OUTLIER) cc_final: 0.7062 (p) REVERT: E 790 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.7120 (mpp) REVERT: E 831 TRP cc_start: 0.7636 (m100) cc_final: 0.7420 (m100) REVERT: E 946 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6230 (pt0) REVERT: E 1522 TYR cc_start: 0.5635 (t80) cc_final: 0.5271 (t80) REVERT: G 103 CYS cc_start: 0.7651 (t) cc_final: 0.6855 (t) REVERT: I 356 ASP cc_start: 0.8154 (t0) cc_final: 0.7653 (t0) REVERT: I 386 ARG cc_start: 0.9147 (ttm110) cc_final: 0.8937 (mtp85) REVERT: I 391 LEU cc_start: 0.9238 (mt) cc_final: 0.8956 (tp) outliers start: 155 outliers final: 113 residues processed: 791 average time/residue: 0.5433 time to fit residues: 741.1486 Evaluate side-chains 772 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 647 time to evaluate : 5.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1221 THR Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1529 MET Chi-restraints excluded: chain B residue 1541 HIS Chi-restraints excluded: chain B residue 1552 LEU Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1802 LEU Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2349 LEU Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 716 ILE Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1512 LEU Chi-restraints excluded: chain F residue 1611 LEU Chi-restraints excluded: chain F residue 1634 THR Chi-restraints excluded: chain F residue 1637 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1515 MET Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2172 LEU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2307 SER Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2548 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 790 MET Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 935 SER Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 946 GLU Chi-restraints excluded: chain E residue 978 THR Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1664 THR Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 384 ASP Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 666 optimal weight: 0.9980 chunk 701 optimal weight: 3.9990 chunk 640 optimal weight: 0.7980 chunk 682 optimal weight: 2.9990 chunk 410 optimal weight: 20.0000 chunk 297 optimal weight: 0.9980 chunk 536 optimal weight: 0.9990 chunk 209 optimal weight: 0.0030 chunk 616 optimal weight: 0.7980 chunk 645 optimal weight: 3.9990 chunk 680 optimal weight: 0.0070 overall best weight: 0.5208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 59658 Z= 0.146 Angle : 0.534 14.978 80992 Z= 0.265 Chirality : 0.039 0.267 9400 Planarity : 0.004 0.055 10390 Dihedral : 3.789 53.052 8280 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 2.28 % Allowed : 16.04 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.10), residues: 7536 helix: 1.64 (0.08), residues: 4760 sheet: -0.26 (0.27), residues: 368 loop : -1.04 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A1269 HIS 0.011 0.001 HIS B2189 PHE 0.030 0.001 PHE E 63 TYR 0.022 0.001 TYR I 326 ARG 0.012 0.000 ARG I 386 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 702 time to evaluate : 5.489 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: B 304 MET cc_start: 0.5821 (tmm) cc_final: 0.5339 (tmm) REVERT: B 311 ARG cc_start: 0.7872 (ptm160) cc_final: 0.7525 (ptm160) REVERT: B 821 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8173 (t80) REVERT: B 853 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.6723 (t80) REVERT: B 1467 MET cc_start: 0.7324 (mtp) cc_final: 0.7124 (mtp) REVERT: B 1529 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.6880 (tmm) REVERT: B 1530 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7441 (mt-10) REVERT: B 1539 ASP cc_start: 0.8016 (t0) cc_final: 0.7626 (t0) REVERT: B 1565 ASP cc_start: 0.8053 (m-30) cc_final: 0.7426 (m-30) REVERT: B 1743 LEU cc_start: 0.8810 (tt) cc_final: 0.8172 (tp) REVERT: B 1747 MET cc_start: 0.8508 (mmm) cc_final: 0.7697 (mpp) REVERT: B 1904 LEU cc_start: 0.9078 (tp) cc_final: 0.8796 (tt) REVERT: B 2175 MET cc_start: 0.8495 (tpp) cc_final: 0.8256 (mmm) REVERT: B 2233 ASN cc_start: 0.8678 (p0) cc_final: 0.8418 (p0) REVERT: D 158 LYS cc_start: 0.6146 (tptt) cc_final: 0.5459 (mmmm) REVERT: D 245 LYS cc_start: 0.6834 (mmtt) cc_final: 0.6483 (mmtt) REVERT: D 273 MET cc_start: 0.8548 (tpp) cc_final: 0.8264 (mmm) REVERT: F 568 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6559 (tm-30) REVERT: F 594 ASP cc_start: 0.8189 (m-30) cc_final: 0.7638 (t0) REVERT: F 716 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8248 (mp) REVERT: F 894 HIS cc_start: 0.7548 (t70) cc_final: 0.7317 (t-90) REVERT: F 1512 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6190 (mp) REVERT: F 1532 GLN cc_start: 0.7458 (tp40) cc_final: 0.7215 (pp30) REVERT: F 1633 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7051 (mp0) REVERT: H 6 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8075 (m-40) REVERT: H 36 VAL cc_start: 0.6158 (OUTLIER) cc_final: 0.5952 (p) REVERT: H 94 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7322 (ttm170) REVERT: A 752 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7852 (mt0) REVERT: A 1289 LEU cc_start: 0.8440 (mm) cc_final: 0.8189 (mt) REVERT: A 1313 MET cc_start: 0.8968 (tmm) cc_final: 0.8569 (tpp) REVERT: A 1478 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 1503 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8010 (pp) REVERT: A 1539 ASP cc_start: 0.8121 (t0) cc_final: 0.7786 (t0) REVERT: A 1873 LEU cc_start: 0.6834 (mm) cc_final: 0.6593 (pp) REVERT: A 2089 MET cc_start: 0.7916 (mpp) cc_final: 0.7512 (mpp) REVERT: A 2161 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7084 (tm-30) REVERT: A 2175 MET cc_start: 0.8299 (mmm) cc_final: 0.8031 (tpp) REVERT: A 2297 ASP cc_start: 0.8533 (p0) cc_final: 0.8148 (p0) REVERT: C 165 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6300 (pp) REVERT: C 213 LYS cc_start: 0.7537 (tptm) cc_final: 0.7084 (ttmt) REVERT: C 255 MET cc_start: 0.7787 (tpt) cc_final: 0.6885 (mmt) REVERT: E 83 ASP cc_start: 0.7932 (m-30) cc_final: 0.7498 (t70) REVERT: E 213 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7627 (tttm) REVERT: E 225 GLU cc_start: 0.7226 (mm-30) cc_final: 0.7014 (mt-10) REVERT: E 240 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.9072 (p) REVERT: E 249 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7208 (mm-30) REVERT: E 366 ASP cc_start: 0.7869 (m-30) cc_final: 0.7338 (t0) REVERT: E 414 ASN cc_start: 0.8171 (t0) cc_final: 0.7815 (t0) REVERT: E 453 MET cc_start: 0.8648 (tpp) cc_final: 0.8330 (mmt) REVERT: E 481 GLU cc_start: 0.8144 (mp0) cc_final: 0.7420 (mp0) REVERT: E 528 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7381 (mp) REVERT: E 529 LEU cc_start: 0.8174 (mt) cc_final: 0.7246 (pp) REVERT: E 671 HIS cc_start: 0.7216 (p-80) cc_final: 0.6779 (p90) REVERT: E 725 THR cc_start: 0.7261 (OUTLIER) cc_final: 0.7003 (p) REVERT: E 790 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7108 (mpp) REVERT: E 831 TRP cc_start: 0.7632 (m100) cc_final: 0.7405 (m100) REVERT: E 946 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6297 (pt0) REVERT: E 1522 TYR cc_start: 0.5569 (t80) cc_final: 0.5303 (t80) REVERT: E 1682 PHE cc_start: 0.7153 (m-10) cc_final: 0.6951 (m-10) REVERT: G 88 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7562 (tp40) REVERT: I 391 LEU cc_start: 0.9226 (mt) cc_final: 0.8944 (tp) REVERT: J 353 GLN cc_start: 0.8206 (tp40) cc_final: 0.7927 (mm-40) outliers start: 135 outliers final: 101 residues processed: 798 average time/residue: 0.5486 time to fit residues: 752.5983 Evaluate side-chains 778 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 661 time to evaluate : 5.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1221 THR Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1529 MET Chi-restraints excluded: chain B residue 1541 HIS Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 1665 ARG Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1802 LEU Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 540 HIS Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 716 ILE Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1512 LEU Chi-restraints excluded: chain F residue 1611 LEU Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1515 MET Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1701 MET Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2307 SER Chi-restraints excluded: chain A residue 2548 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 790 MET Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 935 SER Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 946 GLU Chi-restraints excluded: chain E residue 978 THR Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1664 THR Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 448 optimal weight: 0.4980 chunk 721 optimal weight: 0.9990 chunk 440 optimal weight: 3.9990 chunk 342 optimal weight: 0.7980 chunk 501 optimal weight: 0.9990 chunk 757 optimal weight: 8.9990 chunk 696 optimal weight: 2.9990 chunk 602 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 465 optimal weight: 3.9990 chunk 369 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 947 ASN J 390 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 59658 Z= 0.167 Angle : 0.551 14.862 80992 Z= 0.274 Chirality : 0.039 0.262 9400 Planarity : 0.004 0.057 10390 Dihedral : 3.811 53.123 8280 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Rotamer: Outliers : 2.24 % Allowed : 16.35 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.10), residues: 7536 helix: 1.65 (0.08), residues: 4760 sheet: -0.24 (0.27), residues: 368 loop : -1.05 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A2429 HIS 0.014 0.001 HIS F 540 PHE 0.013 0.001 PHE B1122 TYR 0.025 0.001 TYR B2542 ARG 0.007 0.000 ARG F 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 677 time to evaluate : 5.291 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: B 304 MET cc_start: 0.5840 (tmm) cc_final: 0.5418 (tmm) REVERT: B 311 ARG cc_start: 0.7876 (ptm160) cc_final: 0.7519 (ptm160) REVERT: B 704 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8271 (m) REVERT: B 821 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8113 (t80) REVERT: B 853 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.6913 (t80) REVERT: B 1291 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8080 (mm) REVERT: B 1467 MET cc_start: 0.7345 (mtp) cc_final: 0.7139 (mmp) REVERT: B 1529 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.6871 (tmm) REVERT: B 1530 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7486 (mt-10) REVERT: B 1539 ASP cc_start: 0.8036 (t0) cc_final: 0.7621 (t0) REVERT: B 1565 ASP cc_start: 0.7961 (m-30) cc_final: 0.7325 (m-30) REVERT: B 1743 LEU cc_start: 0.8828 (tt) cc_final: 0.8210 (tp) REVERT: B 1747 MET cc_start: 0.8544 (mmm) cc_final: 0.7740 (mpp) REVERT: B 1904 LEU cc_start: 0.9086 (tp) cc_final: 0.8811 (tt) REVERT: B 2175 MET cc_start: 0.8526 (tpp) cc_final: 0.8278 (mmm) REVERT: B 2233 ASN cc_start: 0.8732 (p0) cc_final: 0.8430 (p0) REVERT: B 2415 MET cc_start: 0.8378 (tpp) cc_final: 0.8172 (tpp) REVERT: D 158 LYS cc_start: 0.6161 (tptt) cc_final: 0.5487 (mmmm) REVERT: D 245 LYS cc_start: 0.6841 (mmtt) cc_final: 0.6476 (mmtt) REVERT: D 273 MET cc_start: 0.8567 (tpp) cc_final: 0.8260 (mmm) REVERT: F 594 ASP cc_start: 0.8201 (m-30) cc_final: 0.7567 (t0) REVERT: F 716 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8315 (mp) REVERT: F 894 HIS cc_start: 0.7450 (t70) cc_final: 0.7241 (t-90) REVERT: F 1512 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6225 (mp) REVERT: F 1532 GLN cc_start: 0.7478 (tp40) cc_final: 0.7225 (pp30) REVERT: F 1633 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7048 (mp0) REVERT: H 6 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8063 (m-40) REVERT: H 36 VAL cc_start: 0.6189 (OUTLIER) cc_final: 0.5950 (p) REVERT: H 94 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7325 (ttm170) REVERT: A 1289 LEU cc_start: 0.8447 (mm) cc_final: 0.8173 (mt) REVERT: A 1313 MET cc_start: 0.8971 (tmm) cc_final: 0.8585 (tpp) REVERT: A 1478 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8213 (tt) REVERT: A 1503 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8023 (pp) REVERT: A 1539 ASP cc_start: 0.8128 (t0) cc_final: 0.7792 (t0) REVERT: A 2089 MET cc_start: 0.7893 (mpp) cc_final: 0.7499 (mpp) REVERT: A 2161 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7089 (tm-30) REVERT: A 2175 MET cc_start: 0.8283 (mmm) cc_final: 0.8009 (tpp) REVERT: A 2297 ASP cc_start: 0.8595 (p0) cc_final: 0.8192 (p0) REVERT: C 165 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6314 (pp) REVERT: C 213 LYS cc_start: 0.7522 (tptm) cc_final: 0.7150 (ttmt) REVERT: C 255 MET cc_start: 0.7746 (tpt) cc_final: 0.6818 (mmt) REVERT: E 83 ASP cc_start: 0.7928 (m-30) cc_final: 0.7611 (t70) REVERT: E 213 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7640 (tttm) REVERT: E 240 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.9077 (p) REVERT: E 249 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7228 (mm-30) REVERT: E 366 ASP cc_start: 0.7875 (m-30) cc_final: 0.7351 (t0) REVERT: E 414 ASN cc_start: 0.8211 (t0) cc_final: 0.7853 (t0) REVERT: E 453 MET cc_start: 0.8662 (tpp) cc_final: 0.8340 (mmt) REVERT: E 481 GLU cc_start: 0.8137 (mp0) cc_final: 0.7913 (mt-10) REVERT: E 528 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7386 (mp) REVERT: E 529 LEU cc_start: 0.8180 (mt) cc_final: 0.7263 (pp) REVERT: E 671 HIS cc_start: 0.7236 (p-80) cc_final: 0.7010 (p-80) REVERT: E 725 THR cc_start: 0.7248 (OUTLIER) cc_final: 0.6991 (p) REVERT: E 790 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7104 (mpp) REVERT: E 831 TRP cc_start: 0.7658 (m100) cc_final: 0.7421 (m100) REVERT: E 946 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6322 (pt0) REVERT: E 1493 MET cc_start: 0.4240 (mtt) cc_final: 0.3882 (mtp) REVERT: E 1522 TYR cc_start: 0.5560 (t80) cc_final: 0.5306 (t80) REVERT: E 1682 PHE cc_start: 0.7127 (m-10) cc_final: 0.6927 (m-10) REVERT: G 88 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7541 (tp40) REVERT: I 385 TYR cc_start: 0.7905 (p90) cc_final: 0.7693 (p90) REVERT: I 391 LEU cc_start: 0.9226 (mt) cc_final: 0.8965 (tp) REVERT: J 353 GLN cc_start: 0.8244 (tp40) cc_final: 0.8011 (mm-40) REVERT: J 366 MET cc_start: 0.7050 (tpp) cc_final: 0.6670 (tpp) outliers start: 133 outliers final: 108 residues processed: 769 average time/residue: 0.5465 time to fit residues: 724.8589 Evaluate side-chains 782 residues out of total 6766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 657 time to evaluate : 5.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1338 ILE Chi-restraints excluded: chain B residue 1380 ILE Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1529 MET Chi-restraints excluded: chain B residue 1541 HIS Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 1665 ARG Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1802 LEU Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 540 HIS Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 716 ILE Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1512 LEU Chi-restraints excluded: chain F residue 1611 LEU Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1515 MET Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1650 MET Chi-restraints excluded: chain A residue 1701 MET Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2172 LEU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2307 SER Chi-restraints excluded: chain A residue 2548 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 790 MET Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 935 SER Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 946 GLU Chi-restraints excluded: chain E residue 978 THR Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1664 THR Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 478 optimal weight: 0.9990 chunk 642 optimal weight: 6.9990 chunk 184 optimal weight: 0.0170 chunk 555 optimal weight: 4.9990 chunk 89 optimal weight: 0.0670 chunk 167 optimal weight: 0.0980 chunk 603 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 620 optimal weight: 40.0000 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.134204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.101377 restraints weight = 121050.111| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.52 r_work: 0.3257 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 59658 Z= 0.173 Angle : 0.550 14.408 80992 Z= 0.273 Chirality : 0.040 0.261 9400 Planarity : 0.004 0.055 10390 Dihedral : 3.828 53.174 8280 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 2.29 % Allowed : 16.28 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.10), residues: 7536 helix: 1.67 (0.08), residues: 4762 sheet: -0.28 (0.27), residues: 368 loop : -1.03 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A2429 HIS 0.012 0.001 HIS B2189 PHE 0.015 0.001 PHE I 371 TYR 0.016 0.001 TYR B 929 ARG 0.007 0.000 ARG F 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13859.70 seconds wall clock time: 242 minutes 40.60 seconds (14560.60 seconds total)