Starting phenix.real_space_refine on Tue Aug 26 20:20:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zj2_60136/08_2025/8zj2_60136.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zj2_60136/08_2025/8zj2_60136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zj2_60136/08_2025/8zj2_60136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zj2_60136/08_2025/8zj2_60136.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zj2_60136/08_2025/8zj2_60136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zj2_60136/08_2025/8zj2_60136.map" } resolution = 4.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2049 atoms to isotropic. 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 P 3 5.49 5 Mg 1 5.21 5 S 215 5.16 5 C 24667 2.51 5 N 6525 2.21 5 O 7176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38587 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 13436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1642, 13436 Classifications: {'peptide': 1642} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1583} Chain: "C" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1385 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain: "F" Number of atoms: 13436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1642, 13436 Classifications: {'peptide': 1642} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1583} Chain: "G" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1385 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain: "E" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1617 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 184} Chain: "A" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5879 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 693} Chain: "D" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1416 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 13, 'TRANS': 167} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.48, per 1000 atoms: 0.19 Number of scatterers: 38587 At special positions: 0 Unit cell: (239.4, 191.52, 162.26, 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) S 215 16.00 P 3 15.00 Mg 1 11.99 O 7176 8.00 N 6525 7.00 C 24667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9072 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 23 sheets defined 56.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'B' and resid 84 through 103 Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.772A pdb=" N VAL B 107 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 132 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 167 through 171 removed outlier: 4.432A pdb=" N GLY B 170 " --> pdb=" O ASP B 167 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN B 171 " --> pdb=" O ASP B 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 167 through 171' Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.520A pdb=" N GLU B 177 " --> pdb=" O ASP B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 205 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 634 through 642 removed outlier: 3.964A pdb=" N LEU B 638 " --> pdb=" O ASN B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 657 through 660 Processing helix chain 'B' and resid 661 through 667 removed outlier: 3.790A pdb=" N LYS B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 683 Processing helix chain 'B' and resid 686 through 705 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.544A pdb=" N GLN B 710 " --> pdb=" O ILE B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 723 Processing helix chain 'B' and resid 728 through 743 removed outlier: 3.638A pdb=" N LYS B 732 " --> pdb=" O LEU B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 779 removed outlier: 4.306A pdb=" N GLU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS B 761 " --> pdb=" O LEU B 757 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR B 762 " --> pdb=" O LYS B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 804 Processing helix chain 'B' and resid 805 through 808 removed outlier: 3.505A pdb=" N GLU B 808 " --> pdb=" O PRO B 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 805 through 808' Processing helix chain 'B' and resid 809 through 820 Processing helix chain 'B' and resid 823 through 828 Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'B' and resid 832 through 846 Processing helix chain 'B' and resid 852 through 866 Processing helix chain 'B' and resid 871 through 889 removed outlier: 3.600A pdb=" N GLU B 876 " --> pdb=" O SER B 872 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) Proline residue: B 880 - end of helix Processing helix chain 'B' and resid 895 through 897 No H-bonds generated for 'chain 'B' and resid 895 through 897' Processing helix chain 'B' and resid 898 through 915 Processing helix chain 'B' and resid 916 through 919 removed outlier: 3.541A pdb=" N GLY B 919 " --> pdb=" O LYS B 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 916 through 919' Processing helix chain 'B' and resid 921 through 943 removed outlier: 5.438A pdb=" N ARG B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 964 removed outlier: 3.617A pdb=" N PHE B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 972 removed outlier: 3.739A pdb=" N TYR B 972 " --> pdb=" O HIS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 998 removed outlier: 3.621A pdb=" N ILE B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1033 removed outlier: 3.543A pdb=" N MET B1033 " --> pdb=" O THR B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1037 Processing helix chain 'B' and resid 1042 through 1055 Processing helix chain 'B' and resid 1058 through 1063 Processing helix chain 'B' and resid 1065 through 1077 Processing helix chain 'B' and resid 1078 through 1094 removed outlier: 4.028A pdb=" N GLU B1082 " --> pdb=" O ASP B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1095 through 1100 removed outlier: 3.709A pdb=" N ILE B1099 " --> pdb=" O PRO B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1114 removed outlier: 4.875A pdb=" N GLY B1107 " --> pdb=" O PRO B1103 " (cutoff:3.500A) Proline residue: B1108 - end of helix removed outlier: 4.136A pdb=" N GLU B1111 " --> pdb=" O GLY B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1125 Processing helix chain 'B' and resid 1125 through 1140 removed outlier: 3.929A pdb=" N PHE B1129 " --> pdb=" O ILE B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1162 Processing helix chain 'B' and resid 1165 through 1183 Processing helix chain 'B' and resid 1185 through 1215 removed outlier: 4.440A pdb=" N SER B1189 " --> pdb=" O TYR B1185 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B1215 " --> pdb=" O ILE B1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1235 Processing helix chain 'B' and resid 1236 through 1254 Processing helix chain 'B' and resid 1256 through 1271 removed outlier: 3.778A pdb=" N LEU B1270 " --> pdb=" O LEU B1266 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B1271 " --> pdb=" O HIS B1267 " (cutoff:3.500A) Processing helix chain 'B' and resid 1292 through 1311 Processing helix chain 'B' and resid 1313 through 1332 removed outlier: 3.994A pdb=" N ALA B1317 " --> pdb=" O MET B1313 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B1323 " --> pdb=" O LYS B1319 " (cutoff:3.500A) Processing helix chain 'B' and resid 1334 through 1355 Processing helix chain 'B' and resid 1390 through 1402 Processing helix chain 'B' and resid 1415 through 1421 removed outlier: 3.609A pdb=" N SER B1420 " --> pdb=" O GLU B1416 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1457 removed outlier: 3.825A pdb=" N LEU B1451 " --> pdb=" O PRO B1447 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B1456 " --> pdb=" O ASN B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1539 Processing helix chain 'B' and resid 1544 through 1556 Processing helix chain 'B' and resid 1561 through 1570 Processing helix chain 'B' and resid 1574 through 1579 Processing helix chain 'B' and resid 1582 through 1611 removed outlier: 3.592A pdb=" N LEU B1588 " --> pdb=" O GLU B1584 " (cutoff:3.500A) Proline residue: B1598 - end of helix Processing helix chain 'B' and resid 1614 through 1635 removed outlier: 4.495A pdb=" N LEU B1618 " --> pdb=" O GLN B1614 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 removed outlier: 4.017A pdb=" N LEU C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 72 removed outlier: 3.848A pdb=" N ARG C 66 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG C 68 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Proline residue: C 69 - end of helix Processing helix chain 'C' and resid 86 through 96 Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 116 through 121 removed outlier: 3.505A pdb=" N ASP C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 131 Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.523A pdb=" N GLY C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 4.248A pdb=" N VAL C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 104 Processing helix chain 'F' and resid 111 through 131 Processing helix chain 'F' and resid 137 through 160 Processing helix chain 'F' and resid 180 through 206 Processing helix chain 'F' and resid 209 through 217 removed outlier: 4.044A pdb=" N GLN F 213 " --> pdb=" O ASP F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 275 removed outlier: 4.231A pdb=" N ASN F 275 " --> pdb=" O GLU F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 291 removed outlier: 3.715A pdb=" N ARG F 291 " --> pdb=" O MET F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 334 Processing helix chain 'F' and resid 378 through 389 Processing helix chain 'F' and resid 409 through 416 Processing helix chain 'F' and resid 521 through 524 Processing helix chain 'F' and resid 537 through 544 Processing helix chain 'F' and resid 583 through 588 Processing helix chain 'F' and resid 591 through 604 Processing helix chain 'F' and resid 634 through 642 Processing helix chain 'F' and resid 648 through 658 removed outlier: 4.131A pdb=" N HIS F 652 " --> pdb=" O GLN F 648 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N MET F 658 " --> pdb=" O LEU F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 661 through 666 Processing helix chain 'F' and resid 668 through 683 Processing helix chain 'F' and resid 686 through 705 Processing helix chain 'F' and resid 706 through 711 removed outlier: 5.467A pdb=" N HIS F 711 " --> pdb=" O LYS F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 712 through 723 Processing helix chain 'F' and resid 728 through 742 Processing helix chain 'F' and resid 746 through 777 removed outlier: 4.540A pdb=" N GLU F 751 " --> pdb=" O SER F 747 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS F 761 " --> pdb=" O LEU F 757 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR F 762 " --> pdb=" O LYS F 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 783 through 804 Processing helix chain 'F' and resid 809 through 831 Proline residue: F 821 - end of helix removed outlier: 3.559A pdb=" N ILE F 824 " --> pdb=" O LEU F 820 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN F 825 " --> pdb=" O PRO F 821 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP F 826 " --> pdb=" O SER F 822 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU F 829 " --> pdb=" O ASN F 825 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL F 830 " --> pdb=" O ASP F 826 " (cutoff:3.500A) Processing helix chain 'F' and resid 832 through 847 removed outlier: 3.778A pdb=" N LEU F 836 " --> pdb=" O ASP F 832 " (cutoff:3.500A) Processing helix chain 'F' and resid 852 through 866 Processing helix chain 'F' and resid 871 through 891 removed outlier: 4.659A pdb=" N GLU F 876 " --> pdb=" O SER F 872 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL F 877 " --> pdb=" O GLU F 873 " (cutoff:3.500A) Proline residue: F 880 - end of helix removed outlier: 3.946A pdb=" N ASP F 891 " --> pdb=" O SER F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 897 No H-bonds generated for 'chain 'F' and resid 895 through 897' Processing helix chain 'F' and resid 898 through 915 Processing helix chain 'F' and resid 921 through 931 Processing helix chain 'F' and resid 932 through 943 Processing helix chain 'F' and resid 949 through 964 removed outlier: 3.761A pdb=" N PHE F 953 " --> pdb=" O HIS F 949 " (cutoff:3.500A) Processing helix chain 'F' and resid 965 through 972 removed outlier: 3.972A pdb=" N TYR F 972 " --> pdb=" O HIS F 968 " (cutoff:3.500A) Processing helix chain 'F' and resid 978 through 998 Processing helix chain 'F' and resid 1006 through 1031 Processing helix chain 'F' and resid 1033 through 1037 Processing helix chain 'F' and resid 1042 through 1055 Processing helix chain 'F' and resid 1059 through 1064 removed outlier: 4.029A pdb=" N PHE F1064 " --> pdb=" O LEU F1061 " (cutoff:3.500A) Processing helix chain 'F' and resid 1065 through 1077 removed outlier: 3.802A pdb=" N ARG F1069 " --> pdb=" O SER F1065 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN F1070 " --> pdb=" O GLN F1066 " (cutoff:3.500A) Processing helix chain 'F' and resid 1078 through 1095 removed outlier: 4.098A pdb=" N GLU F1082 " --> pdb=" O ASP F1078 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY F1095 " --> pdb=" O TRP F1091 " (cutoff:3.500A) Processing helix chain 'F' and resid 1096 through 1098 No H-bonds generated for 'chain 'F' and resid 1096 through 1098' Processing helix chain 'F' and resid 1101 through 1114 removed outlier: 5.060A pdb=" N GLY F1107 " --> pdb=" O PRO F1103 " (cutoff:3.500A) Proline residue: F1108 - end of helix removed outlier: 4.433A pdb=" N GLU F1111 " --> pdb=" O GLY F1107 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F1112 " --> pdb=" O PRO F1108 " (cutoff:3.500A) Processing helix chain 'F' and resid 1118 through 1125 Processing helix chain 'F' and resid 1125 through 1140 removed outlier: 3.686A pdb=" N PHE F1129 " --> pdb=" O ILE F1125 " (cutoff:3.500A) Processing helix chain 'F' and resid 1144 through 1162 removed outlier: 3.840A pdb=" N GLU F1150 " --> pdb=" O MET F1146 " (cutoff:3.500A) Processing helix chain 'F' and resid 1165 through 1183 removed outlier: 3.673A pdb=" N HIS F1183 " --> pdb=" O HIS F1179 " (cutoff:3.500A) Processing helix chain 'F' and resid 1185 through 1215 Processing helix chain 'F' and resid 1216 through 1235 Processing helix chain 'F' and resid 1236 through 1254 Processing helix chain 'F' and resid 1256 through 1271 removed outlier: 3.714A pdb=" N LEU F1270 " --> pdb=" O LEU F1266 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU F1271 " --> pdb=" O HIS F1267 " (cutoff:3.500A) Processing helix chain 'F' and resid 1292 through 1311 Processing helix chain 'F' and resid 1314 through 1332 removed outlier: 3.798A pdb=" N GLU F1323 " --> pdb=" O LYS F1319 " (cutoff:3.500A) Processing helix chain 'F' and resid 1334 through 1355 Processing helix chain 'F' and resid 1390 through 1401 Processing helix chain 'F' and resid 1415 through 1421 removed outlier: 3.665A pdb=" N SER F1420 " --> pdb=" O GLU F1416 " (cutoff:3.500A) Processing helix chain 'F' and resid 1447 through 1457 removed outlier: 3.964A pdb=" N LEU F1451 " --> pdb=" O PRO F1447 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA F1456 " --> pdb=" O ASN F1452 " (cutoff:3.500A) Processing helix chain 'F' and resid 1513 through 1539 Processing helix chain 'F' and resid 1544 through 1556 Processing helix chain 'F' and resid 1561 through 1570 Processing helix chain 'F' and resid 1574 through 1579 Processing helix chain 'F' and resid 1583 through 1610 removed outlier: 4.052A pdb=" N GLU F1587 " --> pdb=" O GLN F1583 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU F1588 " --> pdb=" O GLU F1584 " (cutoff:3.500A) Proline residue: F1598 - end of helix Processing helix chain 'F' and resid 1615 through 1635 Processing helix chain 'G' and resid 15 through 25 removed outlier: 4.033A pdb=" N LEU G 19 " --> pdb=" O ALA G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 67 through 72 Processing helix chain 'G' and resid 86 through 96 Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 116 through 121 removed outlier: 3.659A pdb=" N ASP G 121 " --> pdb=" O LEU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 164 through 175 Processing helix chain 'E' and resid 530 through 540 Processing helix chain 'E' and resid 541 through 559 removed outlier: 3.834A pdb=" N LEU E 545 " --> pdb=" O GLN E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 622 through 627 Processing helix chain 'E' and resid 634 through 638 Processing helix chain 'E' and resid 658 through 674 Processing helix chain 'E' and resid 679 through 696 Processing helix chain 'A' and resid 29 through 41 removed outlier: 3.760A pdb=" N ILE A 33 " --> pdb=" O PRO A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 97 through 112 removed outlier: 4.572A pdb=" N ARG A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 removed outlier: 4.292A pdb=" N GLU A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 140 removed outlier: 3.614A pdb=" N LEU A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 167 removed outlier: 4.899A pdb=" N ILE A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.660A pdb=" N THR A 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE A 176 " --> pdb=" O TRP A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 176' Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.671A pdb=" N ILE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 212 through 221 removed outlier: 3.776A pdb=" N GLN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 4.048A pdb=" N LEU A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 254 Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.674A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 287 through 310 removed outlier: 3.553A pdb=" N ASP A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 333 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.835A pdb=" N SER A 342 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 343 " --> pdb=" O ASN A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 339 through 343' Processing helix chain 'A' and resid 344 through 358 removed outlier: 3.608A pdb=" N LYS A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 377 through 390 Processing helix chain 'A' and resid 391 through 403 Processing helix chain 'A' and resid 412 through 429 Processing helix chain 'A' and resid 442 through 447 removed outlier: 3.706A pdb=" N PHE A 446 " --> pdb=" O HIS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 476 through 493 Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 513 through 528 removed outlier: 4.131A pdb=" N ILE A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.853A pdb=" N ILE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.845A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.569A pdb=" N VAL A 637 " --> pdb=" O ASN A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 674 Processing helix chain 'A' and resid 679 through 696 removed outlier: 3.540A pdb=" N ARG A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'D' and resid 15 through 24 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 86 through 96 removed outlier: 3.751A pdb=" N TYR D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 Processing helix chain 'D' and resid 117 through 120 Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 164 through 178 removed outlier: 3.905A pdb=" N VAL D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.784A pdb=" N LEU B 38 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 46 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N MET B 40 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TRP B 44 " --> pdb=" O MET B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 252 through 253 Processing sheet with id=AA3, first strand: chain 'B' and resid 252 through 253 removed outlier: 3.621A pdb=" N GLU B 240 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 296 " --> pdb=" O MET B 327 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET B 327 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 300 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY B 323 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ARG B 302 " --> pdb=" O PRO B 321 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL B 326 " --> pdb=" O PRO B 347 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N ASP B 328 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 11.452A pdb=" N PHE B 345 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN B 230 " --> pdb=" O TRP B 400 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER B 402 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE B 228 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS B 404 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL B 226 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 406 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU B 224 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 484 through 485 removed outlier: 7.402A pdb=" N THR B 616 " --> pdb=" O LYS B 573 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LYS B 573 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASP B 618 " --> pdb=" O VAL B 571 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N ASP B 568 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LYS B 553 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL B 570 " --> pdb=" O PHE B 551 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N PHE B 551 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG B 532 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 467 " --> pdb=" O ARG B 532 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1428 through 1430 removed outlier: 3.551A pdb=" N PHE B1429 " --> pdb=" O ALA B1364 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1432 through 1433 removed outlier: 6.766A pdb=" N GLN B1460 " --> pdb=" O THR B1491 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 45 removed outlier: 6.878A pdb=" N CYS C 6 " --> pdb=" O TRP C 56 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS C 5 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N LEU C 79 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C 7 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N CYS C 81 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 9 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE C 78 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL C 113 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE C 80 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE C 110 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N LEU C 155 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU C 112 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.940A pdb=" N LEU F 38 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ARG F 46 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N MET F 40 " --> pdb=" O TRP F 44 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N TRP F 44 " --> pdb=" O MET F 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 343 through 347 removed outlier: 4.031A pdb=" N TRP F 400 " --> pdb=" O ASN F 230 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASN F 230 " --> pdb=" O TRP F 400 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N SER F 402 " --> pdb=" O PHE F 228 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N PHE F 228 " --> pdb=" O SER F 402 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LYS F 404 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL F 226 " --> pdb=" O LYS F 404 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU F 406 " --> pdb=" O LEU F 224 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU F 224 " --> pdb=" O LEU F 406 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN F 278 " --> pdb=" O ALA F 426 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA F 428 " --> pdb=" O GLN F 278 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 280 " --> pdb=" O ALA F 428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 252 through 253 Processing sheet with id=AB2, first strand: chain 'F' and resid 252 through 253 removed outlier: 3.607A pdb=" N MET F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 511 through 514 removed outlier: 4.047A pdb=" N GLU F 511 " --> pdb=" O LEU F 450 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 513 " --> pdb=" O VAL F 448 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP F 445 " --> pdb=" O CYS F 627 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 625 " --> pdb=" O TYR F 447 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 470 through 473 removed outlier: 3.521A pdb=" N ILE F 527 " --> pdb=" O VAL F 552 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY F 548 " --> pdb=" O PHE F 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 1429 through 1430 removed outlier: 3.661A pdb=" N PHE F1429 " --> pdb=" O ALA F1364 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE F1380 " --> pdb=" O VAL F1504 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N PHE F1502 " --> pdb=" O THR F1494 " (cutoff:3.500A) removed outlier: 9.922A pdb=" N THR F1494 " --> pdb=" O PHE F1502 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N VAL F1504 " --> pdb=" O ALA F1492 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ALA F1492 " --> pdb=" O VAL F1504 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN F1460 " --> pdb=" O THR F1491 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 41 through 43 removed outlier: 6.679A pdb=" N CYS G 6 " --> pdb=" O TRP G 56 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS G 5 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU G 79 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL G 7 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N CYS G 81 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL G 9 " --> pdb=" O CYS G 81 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE G 111 " --> pdb=" O PHE G 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 578 through 579 Processing sheet with id=AB8, first strand: chain 'E' and resid 616 through 617 Processing sheet with id=AB9, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AC1, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AC2, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AC3, first strand: chain 'A' and resid 578 through 579 Processing sheet with id=AC4, first strand: chain 'A' and resid 616 through 618 removed outlier: 3.766A pdb=" N TYR A 646 " --> pdb=" O CYS A 650 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 650 " --> pdb=" O TYR A 646 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 39 through 46 removed outlier: 3.876A pdb=" N LEU D 53 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN D 54 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS D 6 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP D 56 " --> pdb=" O CYS D 6 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N PHE D 78 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL D 113 " --> pdb=" O PHE D 78 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE D 80 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR D 115 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE D 82 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE D 110 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU D 155 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU D 112 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N CYS D 157 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLY D 114 " --> pdb=" O CYS D 157 " (cutoff:3.500A) 1977 hydrogen bonds defined for protein. 5742 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: 7.80 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10902 1.33 - 1.45: 6979 1.45 - 1.58: 21155 1.58 - 1.70: 5 1.70 - 1.82: 358 Bond restraints: 39399 Sorted by residual: bond pdb=" C LEU B 163 " pdb=" N VAL B 164 " ideal model delta sigma weight residual 1.332 1.277 0.054 1.36e-02 5.41e+03 1.60e+01 bond pdb=" CA LEU B1054 " pdb=" C LEU B1054 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.38e-02 5.25e+03 9.64e+00 bond pdb=" CA ASN B 649 " pdb=" C ASN B 649 " ideal model delta sigma weight residual 1.523 1.486 0.036 1.41e-02 5.03e+03 6.59e+00 bond pdb=" C VAL B1431 " pdb=" N LYS B1432 " ideal model delta sigma weight residual 1.332 1.301 0.032 1.44e-02 4.82e+03 4.79e+00 bond pdb=" CG1 ILE B 863 " pdb=" CD1 ILE B 863 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.76e+00 ... (remaining 39394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 51957 2.71 - 5.42: 1120 5.42 - 8.14: 131 8.14 - 10.85: 20 10.85 - 13.56: 7 Bond angle restraints: 53235 Sorted by residual: angle pdb=" CB ARG F 96 " pdb=" CG ARG F 96 " pdb=" CD ARG F 96 " ideal model delta sigma weight residual 111.30 124.86 -13.56 2.30e+00 1.89e-01 3.48e+01 angle pdb=" N HIS A 89 " pdb=" CA HIS A 89 " pdb=" CB HIS A 89 " ideal model delta sigma weight residual 110.16 117.82 -7.66 1.48e+00 4.57e-01 2.68e+01 angle pdb=" CA MET B 992 " pdb=" CB MET B 992 " pdb=" CG MET B 992 " ideal model delta sigma weight residual 114.10 104.00 10.10 2.00e+00 2.50e-01 2.55e+01 angle pdb=" C LEU F 95 " pdb=" N ARG F 96 " pdb=" CA ARG F 96 " ideal model delta sigma weight residual 120.72 112.29 8.43 1.67e+00 3.59e-01 2.55e+01 angle pdb=" C LEU A 88 " pdb=" N HIS A 89 " pdb=" CA HIS A 89 " ideal model delta sigma weight residual 120.29 113.79 6.50 1.42e+00 4.96e-01 2.10e+01 ... (remaining 53230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.95: 23055 26.95 - 53.90: 922 53.90 - 80.86: 82 80.86 - 107.81: 10 107.81 - 134.76: 2 Dihedral angle restraints: 24071 sinusoidal: 10076 harmonic: 13995 Sorted by residual: dihedral pdb=" CA LYS B 110 " pdb=" C LYS B 110 " pdb=" N LEU B 111 " pdb=" CA LEU B 111 " ideal model delta harmonic sigma weight residual -180.00 -145.73 -34.27 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" C4' GTP D 202 " pdb=" C5' GTP D 202 " pdb=" O5' GTP D 202 " pdb=" PA GTP D 202 " ideal model delta sinusoidal sigma weight residual 260.87 126.11 134.76 1 2.00e+01 2.50e-03 4.09e+01 dihedral pdb=" C8 GTP D 202 " pdb=" C1' GTP D 202 " pdb=" N9 GTP D 202 " pdb=" O4' GTP D 202 " ideal model delta sinusoidal sigma weight residual 104.59 -15.04 119.64 1 2.00e+01 2.50e-03 3.59e+01 ... (remaining 24068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4970 0.072 - 0.143: 881 0.143 - 0.215: 54 0.215 - 0.287: 6 0.287 - 0.359: 2 Chirality restraints: 5913 Sorted by residual: chirality pdb=" CG LEU B1338 " pdb=" CB LEU B1338 " pdb=" CD1 LEU B1338 " pdb=" CD2 LEU B1338 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CB ILE G 137 " pdb=" CA ILE G 137 " pdb=" CG1 ILE G 137 " pdb=" CG2 ILE G 137 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE F1125 " pdb=" CA ILE F1125 " pdb=" CG1 ILE F1125 " pdb=" CG2 ILE F1125 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 5910 not shown) Planarity restraints: 6816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1043 " 0.033 2.00e-02 2.50e+03 2.94e-02 2.16e+01 pdb=" CG TRP B1043 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP B1043 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP B1043 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B1043 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B1043 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B1043 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1043 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1043 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B1043 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 665 " 0.028 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP E 665 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP E 665 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP E 665 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 665 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 665 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP E 665 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 665 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 665 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 665 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 467 " 0.021 2.00e-02 2.50e+03 1.98e-02 9.84e+00 pdb=" CG TRP A 467 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 467 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 467 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 467 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 467 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 467 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 467 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 467 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 467 " 0.001 2.00e-02 2.50e+03 ... (remaining 6813 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 799 2.57 - 3.15: 38525 3.15 - 3.73: 69231 3.73 - 4.32: 96194 4.32 - 4.90: 142945 Nonbonded interactions: 347694 Sorted by model distance: nonbonded pdb="MG MG D 201 " pdb=" O2G GTP D 202 " model vdw 1.984 2.170 nonbonded pdb=" O HIS B1545 " pdb=" OG SER B1548 " model vdw 2.032 3.040 nonbonded pdb="MG MG D 201 " pdb=" O1B GTP D 202 " model vdw 2.046 2.170 nonbonded pdb=" OD1 ASP F 153 " pdb=" NZ LYS F 197 " model vdw 2.067 3.120 nonbonded pdb=" O TYR F1185 " pdb=" OG SER F1188 " model vdw 2.069 3.040 ... (remaining 347689 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 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 30.360 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 : 0.006 0.085 39400 Z= 0.302 Angle : 0.996 13.559 53235 Z= 0.560 Chirality : 0.052 0.359 5913 Planarity : 0.006 0.066 6816 Dihedral : 14.461 134.762 14999 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 44.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.11), residues: 4731 helix: -1.48 (0.09), residues: 2371 sheet: -2.62 (0.21), residues: 511 loop : -2.55 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 94 TYR 0.030 0.003 TYR B1262 PHE 0.045 0.003 PHE B 59 TRP 0.079 0.004 TRP B1043 HIS 0.012 0.002 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00624 (39399) covalent geometry : angle 0.99578 (53235) hydrogen bonds : bond 0.17673 ( 1973) hydrogen bonds : angle 8.05603 ( 5742) Misc. bond : bond 0.00134 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1158 GLU cc_start: 0.8935 (mp0) cc_final: 0.8706 (mp0) REVERT: B 1522 MET cc_start: 0.9111 (ttt) cc_final: 0.8885 (ppp) REVERT: B 1538 TRP cc_start: 0.7358 (t60) cc_final: 0.6727 (t60) REVERT: B 1597 MET cc_start: 0.8817 (mmp) cc_final: 0.8409 (mmp) REVERT: F 306 MET cc_start: 0.3385 (tpt) cc_final: 0.3016 (tpp) REVERT: F 579 MET cc_start: 0.4715 (mmt) cc_final: 0.3930 (mmt) REVERT: F 943 MET cc_start: 0.4527 (ptt) cc_final: 0.3756 (ttp) REVERT: F 1011 MET cc_start: 0.9644 (mmp) cc_final: 0.9425 (mmm) REVERT: F 1435 MET cc_start: 0.7962 (tpt) cc_final: 0.7325 (tpt) REVERT: F 1482 MET cc_start: 0.6918 (mmp) cc_final: 0.6454 (mmm) REVERT: G 45 MET cc_start: 0.7296 (ptp) cc_final: 0.7068 (ptp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1809 time to fit residues: 61.2320 Evaluate side-chains 168 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 0.0670 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 10.0000 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 278 GLN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 ASN ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN B 908 ASN B 946 GLN B1203 ASN ** B1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN F 537 GLN F 743 ASN ** F 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 904 GLN F 908 ASN F1035 GLN ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.072910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.047392 restraints weight = 405156.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.045210 restraints weight = 330180.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.045864 restraints weight = 242227.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.045641 restraints weight = 169340.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.045711 restraints weight = 156737.144| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39400 Z= 0.175 Angle : 0.773 11.094 53235 Z= 0.404 Chirality : 0.047 0.226 5913 Planarity : 0.005 0.065 6816 Dihedral : 7.504 137.747 5171 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.28 % Allowed : 6.86 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.12), residues: 4731 helix: -0.82 (0.10), residues: 2440 sheet: -2.40 (0.21), residues: 536 loop : -2.34 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F1390 TYR 0.021 0.002 TYR B1240 PHE 0.032 0.002 PHE D 37 TRP 0.033 0.002 TRP F1538 HIS 0.008 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00374 (39399) covalent geometry : angle 0.77347 (53235) hydrogen bonds : bond 0.05322 ( 1973) hydrogen bonds : angle 6.41870 ( 5742) Misc. bond : bond 0.00130 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 216 time to evaluate : 0.965 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: B 431 MET cc_start: 0.8452 (mtt) cc_final: 0.8230 (mtt) REVERT: B 595 MET cc_start: 0.8137 (mtt) cc_final: 0.7775 (mtp) REVERT: B 766 PHE cc_start: 0.9413 (m-80) cc_final: 0.8974 (m-10) REVERT: B 1007 MET cc_start: 0.8474 (pmm) cc_final: 0.8132 (pmm) REVERT: B 1131 MET cc_start: 0.8903 (pmm) cc_final: 0.8387 (pmm) REVERT: B 1158 GLU cc_start: 0.8885 (mp0) cc_final: 0.8591 (mp0) REVERT: B 1243 TYR cc_start: 0.8690 (m-80) cc_final: 0.8026 (m-80) REVERT: B 1408 MET cc_start: 0.6662 (mtp) cc_final: 0.6367 (mtp) REVERT: B 1538 TRP cc_start: 0.7572 (t60) cc_final: 0.6963 (t60) REVERT: B 1597 MET cc_start: 0.8776 (mmp) cc_final: 0.8365 (mmp) REVERT: F 579 MET cc_start: 0.5009 (mmt) cc_final: 0.4498 (mmt) REVERT: F 943 MET cc_start: 0.4649 (ptt) cc_final: 0.3630 (ttp) REVERT: F 1011 MET cc_start: 0.9579 (mmp) cc_final: 0.9372 (mmp) REVERT: F 1243 TYR cc_start: 0.8521 (m-80) cc_final: 0.8247 (m-80) REVERT: F 1313 MET cc_start: 0.7732 (tmm) cc_final: 0.7395 (tmm) REVERT: F 1435 MET cc_start: 0.8125 (tpt) cc_final: 0.7537 (tpt) REVERT: F 1482 MET cc_start: 0.7510 (mmp) cc_final: 0.7030 (mmm) REVERT: G 45 MET cc_start: 0.7074 (ptp) cc_final: 0.6758 (ptp) REVERT: E 692 MET cc_start: 0.9005 (mpp) cc_final: 0.8785 (mpp) REVERT: A 481 MET cc_start: 0.1703 (tpt) cc_final: 0.1424 (mmm) outliers start: 12 outliers final: 0 residues processed: 226 average time/residue: 0.1825 time to fit residues: 71.4943 Evaluate side-chains 179 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 311 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 374 optimal weight: 8.9990 chunk 415 optimal weight: 20.0000 chunk 324 optimal weight: 7.9990 chunk 381 optimal weight: 0.0870 chunk 223 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 428 optimal weight: 0.3980 overall best weight: 2.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 HIS F 743 ASN ** F 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1401 GLN ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 464 ASN D 98 HIS D 132 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.072617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.043233 restraints weight = 365223.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.040237 restraints weight = 332747.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.039540 restraints weight = 257808.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.039842 restraints weight = 205613.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.039899 restraints weight = 185569.481| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 39400 Z= 0.175 Angle : 0.741 10.470 53235 Z= 0.386 Chirality : 0.047 0.223 5913 Planarity : 0.005 0.067 6816 Dihedral : 7.272 136.636 5171 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.12 % Allowed : 6.07 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.12), residues: 4731 helix: -0.60 (0.10), residues: 2432 sheet: -2.32 (0.21), residues: 531 loop : -2.24 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F1390 TYR 0.027 0.002 TYR B1566 PHE 0.030 0.002 PHE D 37 TRP 0.022 0.002 TRP F1538 HIS 0.007 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00377 (39399) covalent geometry : angle 0.74143 (53235) hydrogen bonds : bond 0.04980 ( 1973) hydrogen bonds : angle 6.14532 ( 5742) Misc. bond : bond 0.00078 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 219 time to evaluate : 1.074 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: B 766 PHE cc_start: 0.9302 (m-80) cc_final: 0.8848 (m-10) REVERT: B 1007 MET cc_start: 0.8469 (pmm) cc_final: 0.8211 (pmm) REVERT: B 1158 GLU cc_start: 0.8902 (mp0) cc_final: 0.8600 (mp0) REVERT: B 1243 TYR cc_start: 0.8707 (m-80) cc_final: 0.8083 (m-80) REVERT: B 1408 MET cc_start: 0.6953 (mtp) cc_final: 0.6668 (mtp) REVERT: B 1426 MET cc_start: 0.7959 (ppp) cc_final: 0.7504 (ppp) REVERT: B 1538 TRP cc_start: 0.7647 (t60) cc_final: 0.6923 (t60) REVERT: B 1560 MET cc_start: 0.8627 (pmm) cc_final: 0.8112 (pmm) REVERT: B 1597 MET cc_start: 0.8920 (mmp) cc_final: 0.8556 (mmp) REVERT: F 106 TYR cc_start: 0.8566 (p90) cc_final: 0.8351 (p90) REVERT: F 579 MET cc_start: 0.4976 (mmt) cc_final: 0.4392 (mmt) REVERT: F 658 MET cc_start: 0.4113 (mpp) cc_final: 0.3654 (tpt) REVERT: F 943 MET cc_start: 0.4490 (ptt) cc_final: 0.3860 (ttp) REVERT: F 1243 TYR cc_start: 0.8403 (m-80) cc_final: 0.8061 (m-80) REVERT: F 1482 MET cc_start: 0.7814 (mmp) cc_final: 0.7306 (mmm) REVERT: A 208 MET cc_start: 0.4603 (mpp) cc_final: 0.3968 (ptp) outliers start: 5 outliers final: 0 residues processed: 223 average time/residue: 0.1758 time to fit residues: 68.3209 Evaluate side-chains 185 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 270 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 321 optimal weight: 4.9990 chunk 462 optimal weight: 5.9990 chunk 243 optimal weight: 30.0000 chunk 225 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 237 optimal weight: 7.9990 chunk 363 optimal weight: 4.9990 chunk 443 optimal weight: 20.0000 chunk 258 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN ** B 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN F 230 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 743 ASN ** F 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 858 ASN F1035 GLN ** F1179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1531 ASN A 52 GLN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.070204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.038361 restraints weight = 308549.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.036153 restraints weight = 281786.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.036389 restraints weight = 231002.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.036348 restraints weight = 201638.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.036500 restraints weight = 198359.734| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 39400 Z= 0.261 Angle : 0.806 12.559 53235 Z= 0.422 Chirality : 0.049 0.270 5913 Planarity : 0.006 0.081 6816 Dihedral : 7.405 137.078 5171 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 29.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 0.09 % Allowed : 5.49 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.12), residues: 4731 helix: -0.70 (0.10), residues: 2431 sheet: -2.30 (0.21), residues: 529 loop : -2.23 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 329 TYR 0.023 0.002 TYR B1240 PHE 0.024 0.002 PHE A 562 TRP 0.021 0.003 TRP B 98 HIS 0.010 0.002 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00548 (39399) covalent geometry : angle 0.80637 (53235) hydrogen bonds : bond 0.05222 ( 1973) hydrogen bonds : angle 6.30583 ( 5742) Misc. bond : bond 0.00105 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 204 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 306 MET cc_start: 0.1754 (tpp) cc_final: 0.1525 (mmm) REVERT: B 595 MET cc_start: 0.7754 (mtt) cc_final: 0.7420 (mtp) REVERT: B 766 PHE cc_start: 0.9269 (m-80) cc_final: 0.8844 (m-10) REVERT: B 1007 MET cc_start: 0.8344 (pmm) cc_final: 0.7943 (pmm) REVERT: B 1158 GLU cc_start: 0.8853 (mp0) cc_final: 0.8620 (mp0) REVERT: B 1243 TYR cc_start: 0.8691 (m-80) cc_final: 0.7976 (m-80) REVERT: B 1408 MET cc_start: 0.6946 (mtp) cc_final: 0.6644 (mtp) REVERT: B 1522 MET cc_start: 0.8961 (ppp) cc_final: 0.8557 (ppp) REVERT: B 1538 TRP cc_start: 0.7570 (t60) cc_final: 0.7256 (t60) REVERT: B 1560 MET cc_start: 0.8467 (pmm) cc_final: 0.7942 (pmm) REVERT: B 1597 MET cc_start: 0.9073 (mmp) cc_final: 0.8697 (mmp) REVERT: B 1635 LYS cc_start: 0.9059 (mptt) cc_final: 0.8826 (tptp) REVERT: F 555 MET cc_start: 0.0271 (ttm) cc_final: -0.0004 (ttm) REVERT: F 579 MET cc_start: 0.5032 (mmt) cc_final: 0.4600 (mmt) REVERT: F 658 MET cc_start: 0.4114 (mpp) cc_final: 0.3531 (tpt) REVERT: F 1202 GLU cc_start: 0.9345 (OUTLIER) cc_final: 0.9127 (pp20) REVERT: F 1482 MET cc_start: 0.7845 (mmp) cc_final: 0.7386 (mmm) REVERT: A 1 MET cc_start: 0.3400 (tpp) cc_final: 0.3110 (mmp) REVERT: A 208 MET cc_start: 0.4329 (mpp) cc_final: 0.3891 (ptp) outliers start: 4 outliers final: 0 residues processed: 207 average time/residue: 0.1813 time to fit residues: 64.0261 Evaluate side-chains 177 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 67 optimal weight: 0.9990 chunk 237 optimal weight: 30.0000 chunk 395 optimal weight: 0.9990 chunk 353 optimal weight: 7.9990 chunk 467 optimal weight: 30.0000 chunk 227 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 446 optimal weight: 30.0000 chunk 152 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 HIS ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 ASN F 743 ASN ** F 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1044 ASN ** F1179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.072697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.047818 restraints weight = 419442.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.046922 restraints weight = 311211.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.047205 restraints weight = 231378.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.047109 restraints weight = 175635.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.047047 restraints weight = 160141.227| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 39400 Z= 0.176 Angle : 0.741 12.768 53235 Z= 0.383 Chirality : 0.047 0.259 5913 Planarity : 0.005 0.065 6816 Dihedral : 7.215 137.346 5171 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.02 % Allowed : 3.91 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.12), residues: 4731 helix: -0.49 (0.10), residues: 2448 sheet: -2.20 (0.21), residues: 529 loop : -2.22 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F1088 TYR 0.029 0.002 TYR B1566 PHE 0.037 0.002 PHE B 59 TRP 0.016 0.002 TRP C 56 HIS 0.008 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00382 (39399) covalent geometry : angle 0.74146 (53235) hydrogen bonds : bond 0.04732 ( 1973) hydrogen bonds : angle 6.02707 ( 5742) Misc. bond : bond 0.00077 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 1.437 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: B 431 MET cc_start: 0.8498 (mtt) cc_final: 0.8225 (mtt) REVERT: B 764 PHE cc_start: 0.9189 (t80) cc_final: 0.8981 (t80) REVERT: B 766 PHE cc_start: 0.9399 (m-80) cc_final: 0.8945 (m-10) REVERT: B 1158 GLU cc_start: 0.8801 (mp0) cc_final: 0.8515 (mp0) REVERT: B 1243 TYR cc_start: 0.8661 (m-80) cc_final: 0.7824 (m-80) REVERT: B 1408 MET cc_start: 0.6902 (mtp) cc_final: 0.6625 (mtp) REVERT: B 1538 TRP cc_start: 0.7566 (t60) cc_final: 0.7220 (t60) REVERT: B 1560 MET cc_start: 0.8211 (pmm) cc_final: 0.7752 (pmm) REVERT: B 1597 MET cc_start: 0.9022 (mmp) cc_final: 0.8659 (mmp) REVERT: F 89 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7126 (pt0) REVERT: F 106 TYR cc_start: 0.8495 (p90) cc_final: 0.8267 (p90) REVERT: F 555 MET cc_start: 0.0894 (ttm) cc_final: 0.0574 (ttm) REVERT: F 579 MET cc_start: 0.5034 (mmt) cc_final: 0.4628 (mmt) REVERT: F 658 MET cc_start: 0.4101 (mpp) cc_final: 0.3161 (tpt) REVERT: F 1009 MET cc_start: 0.9220 (ppp) cc_final: 0.9014 (ppp) REVERT: F 1482 MET cc_start: 0.7920 (mmp) cc_final: 0.7341 (mmm) REVERT: F 1629 LEU cc_start: 0.9039 (pp) cc_final: 0.8791 (pp) REVERT: F 1637 TYR cc_start: 0.5821 (m-10) cc_final: 0.5452 (m-80) REVERT: E 692 MET cc_start: 0.8989 (mpp) cc_final: 0.8742 (mpp) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.1875 time to fit residues: 72.2606 Evaluate side-chains 181 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 389 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 250 optimal weight: 30.0000 chunk 372 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 295 optimal weight: 5.9990 chunk 446 optimal weight: 2.9990 chunk 437 optimal weight: 6.9990 chunk 309 optimal weight: 0.6980 chunk 212 optimal weight: 30.0000 chunk 454 optimal weight: 6.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 743 ASN ** F 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1014 ASN F1035 GLN ** F1179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.072803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.047106 restraints weight = 419792.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.046699 restraints weight = 277923.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.046801 restraints weight = 225692.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.046619 restraints weight = 157947.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.046744 restraints weight = 131664.658| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39400 Z= 0.166 Angle : 0.728 12.461 53235 Z= 0.376 Chirality : 0.047 0.229 5913 Planarity : 0.005 0.068 6816 Dihedral : 7.075 137.218 5171 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.02 % Allowed : 3.54 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.12), residues: 4731 helix: -0.42 (0.10), residues: 2483 sheet: -2.09 (0.21), residues: 529 loop : -2.22 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 94 TYR 0.049 0.002 TYR F1328 PHE 0.027 0.002 PHE B 59 TRP 0.029 0.002 TRP A 467 HIS 0.007 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00359 (39399) covalent geometry : angle 0.72825 (53235) hydrogen bonds : bond 0.04571 ( 1973) hydrogen bonds : angle 5.87074 ( 5742) Misc. bond : bond 0.00070 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 1.445 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: B 195 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8900 (pt0) REVERT: B 431 MET cc_start: 0.8514 (mtt) cc_final: 0.8241 (mtt) REVERT: B 764 PHE cc_start: 0.9204 (t80) cc_final: 0.8998 (t80) REVERT: B 766 PHE cc_start: 0.9400 (m-80) cc_final: 0.8969 (m-10) REVERT: B 1243 TYR cc_start: 0.8455 (m-80) cc_final: 0.7665 (m-80) REVERT: B 1323 GLU cc_start: 0.8477 (mp0) cc_final: 0.8013 (mp0) REVERT: B 1408 MET cc_start: 0.6962 (mtp) cc_final: 0.6632 (mtp) REVERT: B 1435 MET cc_start: 0.8359 (tpp) cc_final: 0.8142 (tpp) REVERT: B 1538 TRP cc_start: 0.7558 (t60) cc_final: 0.7178 (t60) REVERT: B 1560 MET cc_start: 0.8211 (pmm) cc_final: 0.7802 (pmm) REVERT: F 555 MET cc_start: 0.0743 (ttm) cc_final: 0.0425 (ttm) REVERT: F 579 MET cc_start: 0.4946 (mmt) cc_final: 0.4567 (mmt) REVERT: F 658 MET cc_start: 0.4171 (mpp) cc_final: 0.3490 (tpt) REVERT: F 1009 MET cc_start: 0.9274 (ppp) cc_final: 0.9057 (ppp) REVERT: F 1313 MET cc_start: 0.7434 (tmm) cc_final: 0.7203 (tmm) REVERT: F 1408 MET cc_start: 0.7330 (mpp) cc_final: 0.7121 (mpp) REVERT: F 1435 MET cc_start: 0.8097 (tpt) cc_final: 0.7402 (tpt) REVERT: F 1482 MET cc_start: 0.7912 (mmp) cc_final: 0.7314 (mmm) REVERT: F 1629 LEU cc_start: 0.8999 (pp) cc_final: 0.8790 (pp) REVERT: F 1637 TYR cc_start: 0.5750 (m-10) cc_final: 0.5300 (m-80) REVERT: G 45 MET cc_start: 0.7334 (ptp) cc_final: 0.7056 (ptp) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1825 time to fit residues: 71.5912 Evaluate side-chains 188 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 225 optimal weight: 7.9990 chunk 234 optimal weight: 50.0000 chunk 191 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 323 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 344 optimal weight: 10.0000 chunk 367 optimal weight: 9.9990 chunk 451 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 743 ASN ** F 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1035 GLN ** F1179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1526 ASN E 554 ASN A 52 GLN A 84 ASN A 87 GLN A 268 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.070454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.039152 restraints weight = 322665.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.036766 restraints weight = 286430.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.036785 restraints weight = 204382.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.036643 restraints weight = 170974.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.036438 restraints weight = 176718.791| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 39400 Z= 0.227 Angle : 0.786 12.931 53235 Z= 0.407 Chirality : 0.048 0.286 5913 Planarity : 0.006 0.063 6816 Dihedral : 7.192 137.223 5171 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 27.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.02 % Allowed : 2.58 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.12), residues: 4731 helix: -0.55 (0.10), residues: 2482 sheet: -2.20 (0.21), residues: 542 loop : -2.19 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1627 TYR 0.022 0.002 TYR B1328 PHE 0.028 0.002 PHE B 59 TRP 0.054 0.002 TRP B1043 HIS 0.009 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00479 (39399) covalent geometry : angle 0.78568 (53235) hydrogen bonds : bond 0.04848 ( 1973) hydrogen bonds : angle 6.02758 ( 5742) Misc. bond : bond 0.00081 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 431 MET cc_start: 0.8272 (mtt) cc_final: 0.8063 (mtt) REVERT: B 766 PHE cc_start: 0.9291 (m-80) cc_final: 0.8853 (m-10) REVERT: B 1158 GLU cc_start: 0.8865 (mp0) cc_final: 0.8569 (mp0) REVERT: B 1243 TYR cc_start: 0.8666 (m-80) cc_final: 0.7878 (m-80) REVERT: B 1323 GLU cc_start: 0.8499 (mp0) cc_final: 0.8032 (mp0) REVERT: B 1408 MET cc_start: 0.6981 (mtp) cc_final: 0.6687 (mtp) REVERT: B 1522 MET cc_start: 0.9133 (ppp) cc_final: 0.8704 (ppp) REVERT: B 1538 TRP cc_start: 0.7685 (t60) cc_final: 0.7283 (t60) REVERT: B 1560 MET cc_start: 0.8078 (pmm) cc_final: 0.7726 (pmm) REVERT: F 555 MET cc_start: 0.0806 (ttm) cc_final: 0.0514 (ttm) REVERT: F 579 MET cc_start: 0.4778 (mmt) cc_final: 0.4381 (mmt) REVERT: F 658 MET cc_start: 0.4432 (mpp) cc_final: 0.4061 (tpt) REVERT: F 860 MET cc_start: 0.9014 (pmm) cc_final: 0.8704 (pmm) REVERT: F 1482 MET cc_start: 0.8125 (mmp) cc_final: 0.7527 (mmm) REVERT: F 1637 TYR cc_start: 0.5739 (m-10) cc_final: 0.5382 (m-80) REVERT: E 692 MET cc_start: 0.9052 (mpp) cc_final: 0.8822 (mpp) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.1707 time to fit residues: 63.4441 Evaluate side-chains 183 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 463 optimal weight: 10.0000 chunk 254 optimal weight: 3.9990 chunk 325 optimal weight: 6.9990 chunk 382 optimal weight: 5.9990 chunk 411 optimal weight: 30.0000 chunk 352 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 256 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 743 ASN ** F1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 268 GLN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.071079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.039350 restraints weight = 316652.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.037820 restraints weight = 289512.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.037334 restraints weight = 233430.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.037304 restraints weight = 196802.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.037430 restraints weight = 184393.444| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 39400 Z= 0.197 Angle : 0.762 11.884 53235 Z= 0.395 Chirality : 0.048 0.274 5913 Planarity : 0.005 0.064 6816 Dihedral : 7.142 137.549 5171 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.12), residues: 4731 helix: -0.50 (0.10), residues: 2466 sheet: -2.14 (0.21), residues: 540 loop : -2.14 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1627 TYR 0.032 0.002 TYR B1566 PHE 0.025 0.002 PHE B 114 TRP 0.088 0.003 TRP F 102 HIS 0.009 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00424 (39399) covalent geometry : angle 0.76164 (53235) hydrogen bonds : bond 0.04677 ( 1973) hydrogen bonds : angle 5.97354 ( 5742) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.279 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: B 195 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8932 (pt0) REVERT: B 431 MET cc_start: 0.8392 (mtt) cc_final: 0.8156 (mtt) REVERT: B 766 PHE cc_start: 0.9320 (m-80) cc_final: 0.8878 (m-10) REVERT: B 958 ILE cc_start: 0.9623 (pt) cc_final: 0.9340 (pt) REVERT: B 1132 MET cc_start: 0.8904 (tpt) cc_final: 0.8575 (tmm) REVERT: B 1158 GLU cc_start: 0.8920 (mp0) cc_final: 0.8616 (mp0) REVERT: B 1243 TYR cc_start: 0.8669 (m-80) cc_final: 0.7791 (m-80) REVERT: B 1408 MET cc_start: 0.7010 (mtp) cc_final: 0.6676 (mtp) REVERT: B 1522 MET cc_start: 0.9108 (ppp) cc_final: 0.8706 (ppp) REVERT: B 1538 TRP cc_start: 0.7606 (t60) cc_final: 0.7247 (t60) REVERT: B 1560 MET cc_start: 0.8177 (pmm) cc_final: 0.7757 (pmm) REVERT: F 555 MET cc_start: 0.0772 (ttm) cc_final: 0.0477 (ttm) REVERT: F 579 MET cc_start: 0.4562 (mmt) cc_final: 0.4310 (mmt) REVERT: F 863 ILE cc_start: 0.9091 (pt) cc_final: 0.8881 (mt) REVERT: F 1408 MET cc_start: 0.7540 (mpp) cc_final: 0.7337 (mpp) REVERT: F 1482 MET cc_start: 0.8249 (mmp) cc_final: 0.7764 (mmm) REVERT: F 1637 TYR cc_start: 0.5761 (m-10) cc_final: 0.5483 (m-80) REVERT: A 481 MET cc_start: 0.1530 (tpt) cc_final: 0.1193 (mmm) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1840 time to fit residues: 69.2955 Evaluate side-chains 184 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 332 optimal weight: 9.9990 chunk 428 optimal weight: 30.0000 chunk 145 optimal weight: 0.0870 chunk 144 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 257 optimal weight: 0.9990 chunk 289 optimal weight: 6.9990 chunk 187 optimal weight: 0.6980 chunk 412 optimal weight: 30.0000 chunk 148 optimal weight: 0.9980 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 871 GLN ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1293 GLN ** B1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 743 ASN ** F1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 684 ASN A 52 GLN A 237 GLN A 268 GLN A 287 ASN ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 HIS ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.073453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.042283 restraints weight = 358327.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.041216 restraints weight = 281185.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.041170 restraints weight = 209817.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.040769 restraints weight = 171434.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.040586 restraints weight = 178734.934| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39400 Z= 0.143 Angle : 0.737 12.301 53235 Z= 0.379 Chirality : 0.047 0.202 5913 Planarity : 0.005 0.122 6816 Dihedral : 6.909 137.243 5171 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.12), residues: 4731 helix: -0.29 (0.10), residues: 2483 sheet: -1.96 (0.21), residues: 541 loop : -2.18 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 931 TYR 0.020 0.002 TYR F1289 PHE 0.028 0.002 PHE B 114 TRP 0.073 0.002 TRP F 102 HIS 0.008 0.001 HIS E 624 Details of bonding type rmsd covalent geometry : bond 0.00309 (39399) covalent geometry : angle 0.73650 (53235) hydrogen bonds : bond 0.04326 ( 1973) hydrogen bonds : angle 5.68160 ( 5742) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.276 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: B 764 PHE cc_start: 0.9165 (t80) cc_final: 0.8959 (t80) REVERT: B 766 PHE cc_start: 0.9318 (m-80) cc_final: 0.8866 (m-10) REVERT: B 914 ASP cc_start: 0.8698 (t70) cc_final: 0.8468 (t0) REVERT: B 958 ILE cc_start: 0.9657 (pt) cc_final: 0.9384 (pt) REVERT: B 1132 MET cc_start: 0.8866 (tpt) cc_final: 0.8587 (tpp) REVERT: B 1158 GLU cc_start: 0.8875 (mp0) cc_final: 0.8558 (mp0) REVERT: B 1172 LEU cc_start: 0.9300 (mt) cc_final: 0.8938 (mt) REVERT: B 1201 LEU cc_start: 0.9488 (mm) cc_final: 0.9266 (mt) REVERT: B 1243 TYR cc_start: 0.8629 (m-80) cc_final: 0.7814 (m-80) REVERT: B 1408 MET cc_start: 0.6992 (mtp) cc_final: 0.6757 (mtp) REVERT: B 1522 MET cc_start: 0.9058 (ppp) cc_final: 0.8643 (ppp) REVERT: B 1538 TRP cc_start: 0.7565 (t60) cc_final: 0.7080 (t60) REVERT: B 1560 MET cc_start: 0.8050 (pmm) cc_final: 0.7664 (pmm) REVERT: F 551 PHE cc_start: -0.1028 (p90) cc_final: -0.2750 (p90) REVERT: F 555 MET cc_start: 0.0854 (ttm) cc_final: 0.0446 (ttm) REVERT: F 579 MET cc_start: 0.4608 (mmt) cc_final: 0.3321 (mmt) REVERT: F 863 ILE cc_start: 0.9040 (pt) cc_final: 0.8824 (mt) REVERT: F 943 MET cc_start: 0.4944 (ptt) cc_final: 0.4207 (ptt) REVERT: F 1435 MET cc_start: 0.7908 (tpt) cc_final: 0.7255 (tpt) REVERT: F 1482 MET cc_start: 0.8336 (mmp) cc_final: 0.7780 (mmm) REVERT: E 677 MET cc_start: 0.5356 (mmp) cc_final: 0.4519 (mmp) REVERT: A 22 MET cc_start: 0.5053 (tpp) cc_final: 0.4803 (pmm) REVERT: A 481 MET cc_start: 0.1738 (tpt) cc_final: 0.1481 (mmm) REVERT: A 692 MET cc_start: 0.8922 (ppp) cc_final: 0.8528 (tmm) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.1750 time to fit residues: 70.5214 Evaluate side-chains 196 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 84 optimal weight: 0.5980 chunk 381 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 234 optimal weight: 50.0000 chunk 256 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 389 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 354 optimal weight: 0.9980 chunk 439 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1267 HIS B1293 GLN ** B1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 74 GLN F 109 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 743 ASN ** F1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 268 GLN A 340 ASN A 601 HIS ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.072696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.041507 restraints weight = 352638.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.040916 restraints weight = 288389.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.040558 restraints weight = 229966.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.039994 restraints weight = 193655.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.039971 restraints weight = 189594.305| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39400 Z= 0.149 Angle : 0.726 10.100 53235 Z= 0.375 Chirality : 0.047 0.261 5913 Planarity : 0.005 0.117 6816 Dihedral : 6.810 136.760 5171 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.02 % Allowed : 0.54 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.12), residues: 4731 helix: -0.22 (0.10), residues: 2483 sheet: -1.87 (0.21), residues: 540 loop : -2.17 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 875 TYR 0.021 0.002 TYR F1289 PHE 0.027 0.002 PHE F1017 TRP 0.073 0.002 TRP F 102 HIS 0.009 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00324 (39399) covalent geometry : angle 0.72627 (53235) hydrogen bonds : bond 0.04310 ( 1973) hydrogen bonds : angle 5.66708 ( 5742) Misc. bond : bond 0.00073 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9462 Ramachandran restraints generated. 4731 Oldfield, 0 Emsley, 4731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 1.252 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 431 MET cc_start: 0.8597 (mtm) cc_final: 0.8376 (mtt) REVERT: B 766 PHE cc_start: 0.9328 (m-80) cc_final: 0.8865 (m-10) REVERT: B 914 ASP cc_start: 0.8772 (t70) cc_final: 0.8517 (t0) REVERT: B 958 ILE cc_start: 0.9704 (pt) cc_final: 0.9407 (pt) REVERT: B 1105 MET cc_start: 0.8906 (tmm) cc_final: 0.8653 (tmm) REVERT: B 1132 MET cc_start: 0.8848 (tpt) cc_final: 0.8572 (tpp) REVERT: B 1158 GLU cc_start: 0.8829 (mp0) cc_final: 0.8518 (mp0) REVERT: B 1201 LEU cc_start: 0.9391 (mm) cc_final: 0.9149 (mt) REVERT: B 1243 TYR cc_start: 0.8706 (m-80) cc_final: 0.7860 (m-80) REVERT: B 1408 MET cc_start: 0.7029 (mtp) cc_final: 0.6825 (mtp) REVERT: B 1538 TRP cc_start: 0.7664 (t60) cc_final: 0.7188 (t60) REVERT: B 1560 MET cc_start: 0.8065 (pmm) cc_final: 0.7650 (pmm) REVERT: F 120 MET cc_start: 0.7778 (mmm) cc_final: 0.6828 (mtt) REVERT: F 551 PHE cc_start: -0.0592 (p90) cc_final: -0.2229 (p90) REVERT: F 555 MET cc_start: 0.0887 (ttm) cc_final: 0.0484 (ttm) REVERT: F 579 MET cc_start: 0.4379 (mmt) cc_final: 0.3112 (mmt) REVERT: F 863 ILE cc_start: 0.9055 (pt) cc_final: 0.8854 (mt) REVERT: F 943 MET cc_start: 0.4828 (ptt) cc_final: 0.3918 (ptt) REVERT: F 1009 MET cc_start: 0.9272 (ppp) cc_final: 0.9033 (ppp) REVERT: F 1482 MET cc_start: 0.8316 (mmp) cc_final: 0.7749 (mmm) REVERT: A 1 MET cc_start: 0.5498 (mmm) cc_final: 0.5222 (mmm) REVERT: A 22 MET cc_start: 0.4779 (tpp) cc_final: 0.4475 (pmm) REVERT: A 467 TRP cc_start: 0.0147 (m-10) cc_final: -0.0055 (m-10) REVERT: A 481 MET cc_start: 0.1739 (tpt) cc_final: 0.1327 (mmm) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1834 time to fit residues: 71.1489 Evaluate side-chains 189 residues out of total 4299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 222 optimal weight: 30.0000 chunk 360 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 333 optimal weight: 3.9990 chunk 224 optimal weight: 30.0000 chunk 209 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 370 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 296 optimal weight: 0.8980 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 ASN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1293 GLN ** B1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 743 ASN ** F1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 268 GLN ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.070666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.038890 restraints weight = 312989.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.036881 restraints weight = 290064.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.037090 restraints weight = 239221.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.036812 restraints weight = 214255.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.036876 restraints weight = 205356.018| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 39400 Z= 0.208 Angle : 0.781 13.161 53235 Z= 0.406 Chirality : 0.048 0.289 5913 Planarity : 0.006 0.115 6816 Dihedral : 6.967 136.673 5171 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.12), residues: 4731 helix: -0.38 (0.10), residues: 2468 sheet: -2.01 (0.21), residues: 549 loop : -2.09 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG F 935 TYR 0.044 0.002 TYR F1328 PHE 0.030 0.002 PHE F1308 TRP 0.070 0.003 TRP F 102 HIS 0.009 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00444 (39399) covalent geometry : angle 0.78122 (53235) hydrogen bonds : bond 0.04607 ( 1973) hydrogen bonds : angle 5.85672 ( 5742) Misc. bond : bond 0.00081 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8406.68 seconds wall clock time: 145 minutes 42.76 seconds (8742.76 seconds total)