Starting phenix.real_space_refine on Fri May 30 07:38:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjk_60148/05_2025/8zjk_60148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjk_60148/05_2025/8zjk_60148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zjk_60148/05_2025/8zjk_60148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjk_60148/05_2025/8zjk_60148.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjk_60148/05_2025/8zjk_60148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjk_60148/05_2025/8zjk_60148.cif" } resolution = 4.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 21052 2.51 5 N 5538 2.21 5 O 6092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.58s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32858 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1608 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 183} 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: "D" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1608 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "E" 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: "F" 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} Time building chain proxies: 17.98, per 1000 atoms: 0.55 Number of scatterers: 32858 At special positions: 0 Unit cell: (244.72, 166.25, 156.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 6092 8.00 N 5538 7.00 C 21052 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=0, symmetry=0 Time building additional restraints: 9.40 Conformation dependent library (CDL) restraints added in 4.2 seconds 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7696 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 20 sheets defined 55.2% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'A' and resid 530 through 540 Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.843A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.541A pdb=" N ASP A 612 " --> pdb=" O PRO A 609 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 613 " --> pdb=" O VAL A 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 609 through 613' 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 Processing helix chain 'A' and resid 658 through 674 Processing helix chain 'A' and resid 679 through 696 Processing helix chain 'B' and resid 84 through 107 removed outlier: 4.018A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 removed outlier: 4.137A pdb=" N SER B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 168 through 172 removed outlier: 4.277A pdb=" N ILE B 172 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 205 removed outlier: 4.158A pdb=" N LYS B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 273 through 276 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.717A pdb=" N GLN B 361 " --> pdb=" O ARG B 358 " (cutoff:3.500A) 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 577 through 580 Processing helix chain 'B' and resid 581 through 586 removed outlier: 3.511A pdb=" N LEU B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 634 through 642 removed outlier: 3.509A pdb=" N LEU B 638 " --> pdb=" O ASN B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 658 removed outlier: 3.537A pdb=" N LYS B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 668 removed outlier: 3.622A pdb=" N LYS B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 684 Processing helix chain 'B' and resid 686 through 705 Processing helix chain 'B' and resid 709 through 711 No H-bonds generated for 'chain 'B' and resid 709 through 711' Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 728 through 743 removed outlier: 3.736A pdb=" N LYS B 732 " --> pdb=" O LEU B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 759 removed outlier: 3.971A pdb=" N GLU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 778 Processing helix chain 'B' and resid 783 through 804 Processing helix chain 'B' and resid 805 through 830 removed outlier: 4.299A pdb=" N ALA B 809 " --> pdb=" O PRO B 805 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS B 811 " --> pdb=" O GLU B 807 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Proline residue: B 821 - end of helix removed outlier: 3.878A pdb=" N ILE B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASP B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 846 Processing helix chain 'B' and resid 852 through 866 Processing helix chain 'B' and resid 874 through 889 Proline residue: B 880 - end of helix Processing helix chain 'B' and resid 898 through 915 Processing helix chain 'B' and resid 921 through 943 removed outlier: 5.774A pdb=" N ARG B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ARG B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 964 removed outlier: 3.730A pdb=" N PHE B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 973 removed outlier: 3.849A pdb=" N TYR B 972 " --> pdb=" O HIS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 976 No H-bonds generated for 'chain 'B' and resid 974 through 976' Processing helix chain 'B' and resid 978 through 998 removed outlier: 3.571A pdb=" N ILE B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1033 removed outlier: 3.793A pdb=" N MET B1033 " --> pdb=" O THR B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1054 Processing helix chain 'B' and resid 1058 through 1064 Processing helix chain 'B' and resid 1065 through 1076 removed outlier: 3.822A pdb=" N ARG B1069 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1095 removed outlier: 3.700A pdb=" N GLU B1082 " --> pdb=" O ASP B1078 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY B1095 " --> pdb=" O TRP B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1100 removed outlier: 3.897A pdb=" N ILE B1099 " --> pdb=" O PRO B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1106 removed outlier: 3.764A pdb=" N MET B1105 " --> pdb=" O PHE B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1106 through 1114 removed outlier: 3.821A pdb=" N LEU B1110 " --> pdb=" O VAL B1106 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU B1111 " --> pdb=" O GLY B1107 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL B1112 " --> pdb=" O PRO B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1139 Proline residue: B1126 - end of helix removed outlier: 3.638A pdb=" N PHE B1129 " --> pdb=" O ILE B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1161 removed outlier: 3.709A pdb=" N GLU B1150 " --> pdb=" O MET B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1183 removed outlier: 3.536A pdb=" N LYS B1182 " --> pdb=" O GLU B1178 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS B1183 " --> pdb=" O HIS B1179 " (cutoff:3.500A) Processing helix chain 'B' and resid 1184 through 1215 removed outlier: 3.566A 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 1255 Processing helix chain 'B' and resid 1256 through 1271 removed outlier: 3.817A pdb=" N LEU B1270 " --> pdb=" O LEU B1266 " (cutoff:3.500A) removed outlier: 4.048A 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: 4.151A pdb=" N ALA B1317 " --> pdb=" O MET B1313 " (cutoff:3.500A) removed outlier: 3.559A 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 Processing helix chain 'B' and resid 1447 through 1457 removed outlier: 4.089A pdb=" N LEU B1451 " --> pdb=" O PRO B1447 " (cutoff:3.500A) removed outlier: 3.953A 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 1572 through 1579 Processing helix chain 'B' and resid 1580 through 1584 removed outlier: 3.985A pdb=" N GLU B1584 " --> pdb=" O GLU B1581 " (cutoff:3.500A) Processing helix chain 'B' and resid 1585 through 1611 Proline residue: B1598 - end of helix Processing helix chain 'B' and resid 1614 through 1635 removed outlier: 4.177A pdb=" N LEU B1618 " --> pdb=" O GLN B1614 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 removed outlier: 3.790A pdb=" N LEU C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.763A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 67 through 72' 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: 3.948A pdb=" N ASP C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.651A pdb=" N GLY C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 4.052A pdb=" N VAL C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 540 Processing helix chain 'D' and resid 541 through 559 removed outlier: 3.843A pdb=" N LEU D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.541A pdb=" N ASP D 612 " --> pdb=" O PRO D 609 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 613 " --> pdb=" O VAL D 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 609 through 613' Processing helix chain 'D' and resid 620 through 622 No H-bonds generated for 'chain 'D' and resid 620 through 622' Processing helix chain 'D' and resid 634 through 638 Processing helix chain 'D' and resid 658 through 674 Processing helix chain 'D' and resid 679 through 696 Processing helix chain 'E' and resid 84 through 107 removed outlier: 4.018A pdb=" N VAL E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 133 removed outlier: 4.136A pdb=" N SER E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 168 through 172 removed outlier: 4.277A pdb=" N ILE E 172 " --> pdb=" O ASN E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 205 removed outlier: 4.158A pdb=" N LYS E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER E 203 " --> pdb=" O GLN E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 217 Processing helix chain 'E' and resid 273 through 276 Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 329 through 334 Processing helix chain 'E' and resid 357 through 361 removed outlier: 3.716A pdb=" N GLN E 361 " --> pdb=" O ARG E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 389 Processing helix chain 'E' and resid 409 through 417 Processing helix chain 'E' and resid 521 through 523 No H-bonds generated for 'chain 'E' and resid 521 through 523' Processing helix chain 'E' and resid 537 through 544 Processing helix chain 'E' and resid 577 through 580 Processing helix chain 'E' and resid 581 through 586 removed outlier: 3.511A pdb=" N LEU E 586 " --> pdb=" O ALA E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 602 Processing helix chain 'E' and resid 634 through 642 removed outlier: 3.508A pdb=" N LEU E 638 " --> pdb=" O ASN E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 658 removed outlier: 3.537A pdb=" N LYS E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET E 658 " --> pdb=" O LEU E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 668 removed outlier: 3.622A pdb=" N LYS E 667 " --> pdb=" O GLY E 663 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE E 668 " --> pdb=" O GLU E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 684 Processing helix chain 'E' and resid 686 through 705 Processing helix chain 'E' and resid 709 through 711 No H-bonds generated for 'chain 'E' and resid 709 through 711' Processing helix chain 'E' and resid 712 through 722 Processing helix chain 'E' and resid 728 through 743 removed outlier: 3.736A pdb=" N LYS E 732 " --> pdb=" O LEU E 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 759 removed outlier: 3.971A pdb=" N GLU E 751 " --> pdb=" O SER E 747 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 778 Processing helix chain 'E' and resid 783 through 804 Processing helix chain 'E' and resid 805 through 830 removed outlier: 4.299A pdb=" N ALA E 809 " --> pdb=" O PRO E 805 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS E 811 " --> pdb=" O GLU E 807 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE E 812 " --> pdb=" O GLU E 808 " (cutoff:3.500A) Proline residue: E 821 - end of helix removed outlier: 3.879A pdb=" N ILE E 824 " --> pdb=" O LEU E 820 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN E 825 " --> pdb=" O PRO E 821 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASP E 826 " --> pdb=" O SER E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 832 through 846 Processing helix chain 'E' and resid 852 through 866 Processing helix chain 'E' and resid 874 through 889 Proline residue: E 880 - end of helix Processing helix chain 'E' and resid 898 through 915 Processing helix chain 'E' and resid 921 through 943 removed outlier: 5.774A pdb=" N ARG E 934 " --> pdb=" O GLU E 930 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG E 935 " --> pdb=" O ARG E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 949 through 964 removed outlier: 3.730A pdb=" N PHE E 953 " --> pdb=" O HIS E 949 " (cutoff:3.500A) Processing helix chain 'E' and resid 965 through 973 removed outlier: 3.848A pdb=" N TYR E 972 " --> pdb=" O HIS E 968 " (cutoff:3.500A) Processing helix chain 'E' and resid 974 through 976 No H-bonds generated for 'chain 'E' and resid 974 through 976' Processing helix chain 'E' and resid 978 through 998 removed outlier: 3.571A pdb=" N ILE E 982 " --> pdb=" O THR E 978 " (cutoff:3.500A) Processing helix chain 'E' and resid 1006 through 1033 removed outlier: 3.793A pdb=" N MET E1033 " --> pdb=" O THR E1029 " (cutoff:3.500A) Processing helix chain 'E' and resid 1042 through 1054 Processing helix chain 'E' and resid 1058 through 1064 Processing helix chain 'E' and resid 1065 through 1076 removed outlier: 3.822A pdb=" N ARG E1069 " --> pdb=" O SER E1065 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN E1070 " --> pdb=" O GLN E1066 " (cutoff:3.500A) Processing helix chain 'E' and resid 1078 through 1095 removed outlier: 3.701A pdb=" N GLU E1082 " --> pdb=" O ASP E1078 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY E1095 " --> pdb=" O TRP E1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 1096 through 1100 removed outlier: 3.897A pdb=" N ILE E1099 " --> pdb=" O PRO E1096 " (cutoff:3.500A) Processing helix chain 'E' and resid 1101 through 1106 removed outlier: 3.763A pdb=" N MET E1105 " --> pdb=" O PHE E1101 " (cutoff:3.500A) Processing helix chain 'E' and resid 1106 through 1114 removed outlier: 3.820A pdb=" N LEU E1110 " --> pdb=" O VAL E1106 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU E1111 " --> pdb=" O GLY E1107 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL E1112 " --> pdb=" O PRO E1108 " (cutoff:3.500A) Processing helix chain 'E' and resid 1118 through 1139 Proline residue: E1126 - end of helix removed outlier: 3.638A pdb=" N PHE E1129 " --> pdb=" O ILE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1144 through 1161 removed outlier: 3.710A pdb=" N GLU E1150 " --> pdb=" O MET E1146 " (cutoff:3.500A) Processing helix chain 'E' and resid 1165 through 1183 removed outlier: 3.535A pdb=" N LYS E1182 " --> pdb=" O GLU E1178 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS E1183 " --> pdb=" O HIS E1179 " (cutoff:3.500A) Processing helix chain 'E' and resid 1184 through 1215 removed outlier: 3.565A pdb=" N GLU E1215 " --> pdb=" O ILE E1211 " (cutoff:3.500A) Processing helix chain 'E' and resid 1216 through 1235 Processing helix chain 'E' and resid 1236 through 1255 Processing helix chain 'E' and resid 1256 through 1271 removed outlier: 3.816A pdb=" N LEU E1270 " --> pdb=" O LEU E1266 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU E1271 " --> pdb=" O HIS E1267 " (cutoff:3.500A) Processing helix chain 'E' and resid 1292 through 1311 Processing helix chain 'E' and resid 1313 through 1332 removed outlier: 4.152A pdb=" N ALA E1317 " --> pdb=" O MET E1313 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU E1323 " --> pdb=" O LYS E1319 " (cutoff:3.500A) Processing helix chain 'E' and resid 1334 through 1355 Processing helix chain 'E' and resid 1390 through 1402 Processing helix chain 'E' and resid 1415 through 1421 Processing helix chain 'E' and resid 1447 through 1457 removed outlier: 4.089A pdb=" N LEU E1451 " --> pdb=" O PRO E1447 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA E1456 " --> pdb=" O ASN E1452 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1539 Processing helix chain 'E' and resid 1544 through 1556 Processing helix chain 'E' and resid 1561 through 1570 Processing helix chain 'E' and resid 1572 through 1579 Processing helix chain 'E' and resid 1580 through 1584 removed outlier: 3.983A pdb=" N GLU E1584 " --> pdb=" O GLU E1581 " (cutoff:3.500A) Processing helix chain 'E' and resid 1585 through 1611 Proline residue: E1598 - end of helix Processing helix chain 'E' and resid 1614 through 1635 removed outlier: 4.176A pdb=" N LEU E1618 " --> pdb=" O GLN E1614 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 removed outlier: 3.790A pdb=" N LEU F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 66 Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.763A pdb=" N SER F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 72' Processing helix chain 'F' and resid 86 through 96 Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 116 through 121 removed outlier: 3.948A pdb=" N ASP F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 138 through 150 removed outlier: 3.651A pdb=" N GLY F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 177 removed outlier: 4.052A pdb=" N VAL F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA2, first strand: chain 'A' and resid 578 through 579 Processing sheet with id=AA3, first strand: chain 'A' and resid 616 through 618 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'B' and resid 252 through 253 Processing sheet with id=AA6, first strand: chain 'B' and resid 252 through 253 removed outlier: 6.942A pdb=" N LEU B 296 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL B 326 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS B 298 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL B 324 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE B 300 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 326 " --> pdb=" O PRO B 347 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ASP B 328 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 10.478A pdb=" N PHE B 345 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN B 230 " --> pdb=" O TRP B 400 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER B 402 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N PHE B 228 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LYS B 404 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL B 226 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 406 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU B 224 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN B 278 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ALA B 428 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL B 280 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 484 through 485 removed outlier: 7.029A pdb=" N CYS B 508 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N HIS B 452 " --> pdb=" O CYS B 508 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU B 450 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 512 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL B 448 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS B 514 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE B 446 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN B 621 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY B 453 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER B 619 " --> pdb=" O GLY B 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 495 through 497 removed outlier: 3.527A pdb=" N ARG B 532 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 548 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1428 through 1430 removed outlier: 6.068A pdb=" N ILE B1380 " --> pdb=" O VAL B1504 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N PHE B1502 " --> pdb=" O THR B1494 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N THR B1494 " --> pdb=" O PHE B1502 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N VAL B1504 " --> pdb=" O ALA B1492 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ALA B1492 " --> pdb=" O VAL B1504 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN B1460 " --> pdb=" O THR B1491 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 40 through 45 removed outlier: 7.148A pdb=" N CYS C 6 " --> pdb=" O TRP C 56 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LYS C 5 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU C 79 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL C 7 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N CYS C 81 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C 111 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE C 110 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N LEU C 155 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU C 112 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 561 through 563 Processing sheet with id=AB3, first strand: chain 'D' and resid 578 through 579 Processing sheet with id=AB4, first strand: chain 'D' and resid 616 through 618 Processing sheet with id=AB5, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AB6, first strand: chain 'E' and resid 252 through 253 Processing sheet with id=AB7, first strand: chain 'E' and resid 252 through 253 removed outlier: 6.943A pdb=" N LEU E 296 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL E 326 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS E 298 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL E 324 " --> pdb=" O CYS E 298 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE E 300 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL E 326 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ASP E 328 " --> pdb=" O PHE E 345 " (cutoff:3.500A) removed outlier: 10.479A pdb=" N PHE E 345 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN E 230 " --> pdb=" O TRP E 400 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER E 402 " --> pdb=" O PHE E 228 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N PHE E 228 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LYS E 404 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL E 226 " --> pdb=" O LYS E 404 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU E 406 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU E 224 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN E 278 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA E 428 " --> pdb=" O GLN E 278 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL E 280 " --> pdb=" O ALA E 428 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 484 through 485 removed outlier: 7.030A pdb=" N CYS E 508 " --> pdb=" O HIS E 452 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS E 452 " --> pdb=" O CYS E 508 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU E 450 " --> pdb=" O TYR E 510 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR E 512 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL E 448 " --> pdb=" O THR E 512 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS E 514 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE E 446 " --> pdb=" O LYS E 514 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN E 621 " --> pdb=" O ILE E 451 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY E 453 " --> pdb=" O SER E 619 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER E 619 " --> pdb=" O GLY E 453 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 495 through 497 removed outlier: 3.527A pdb=" N ARG E 532 " --> pdb=" O GLU E 467 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY E 548 " --> pdb=" O PHE E 531 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 1428 through 1430 removed outlier: 6.067A pdb=" N ILE E1380 " --> pdb=" O VAL E1504 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N PHE E1502 " --> pdb=" O THR E1494 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N THR E1494 " --> pdb=" O PHE E1502 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N VAL E1504 " --> pdb=" O ALA E1492 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ALA E1492 " --> pdb=" O VAL E1504 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN E1460 " --> pdb=" O THR E1491 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 40 through 45 removed outlier: 7.148A pdb=" N CYS F 6 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LYS F 5 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU F 79 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL F 7 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N CYS F 81 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE F 111 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE F 110 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N LEU F 155 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU F 112 " --> pdb=" O LEU F 155 " (cutoff:3.500A) 1689 hydrogen bonds defined for protein. 4893 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: 13.65 Time building geometry restraints manager: 10.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.19: 2 1.19 - 1.34: 10658 1.34 - 1.50: 9107 1.50 - 1.66: 13495 1.66 - 1.82: 294 Bond restraints: 33556 Sorted by residual: bond pdb=" CG PRO E 463 " pdb=" CD PRO E 463 " ideal model delta sigma weight residual 1.503 1.029 0.474 3.40e-02 8.65e+02 1.94e+02 bond pdb=" CG PRO B 463 " pdb=" CD PRO B 463 " ideal model delta sigma weight residual 1.503 1.030 0.473 3.40e-02 8.65e+02 1.93e+02 bond pdb=" N PRO B 463 " pdb=" CD PRO B 463 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.08e+01 bond pdb=" C VAL B1431 " pdb=" N LYS B1432 " ideal model delta sigma weight residual 1.331 1.278 0.053 1.63e-02 3.76e+03 1.08e+01 bond pdb=" N PRO E 463 " pdb=" CD PRO E 463 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.06e+01 ... (remaining 33551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.24: 45235 5.24 - 10.48: 73 10.48 - 15.72: 10 15.72 - 20.96: 0 20.96 - 26.21: 6 Bond angle restraints: 45324 Sorted by residual: angle pdb=" N PRO B 463 " pdb=" CD PRO B 463 " pdb=" CG PRO B 463 " ideal model delta sigma weight residual 103.20 77.21 25.99 1.50e+00 4.44e-01 3.00e+02 angle pdb=" N PRO E 463 " pdb=" CD PRO E 463 " pdb=" CG PRO E 463 " ideal model delta sigma weight residual 103.20 77.26 25.94 1.50e+00 4.44e-01 2.99e+02 angle pdb=" CA PRO B 463 " pdb=" CB PRO B 463 " pdb=" CG PRO B 463 " ideal model delta sigma weight residual 104.50 81.93 22.57 1.90e+00 2.77e-01 1.41e+02 angle pdb=" CA PRO E 463 " pdb=" CB PRO E 463 " pdb=" CG PRO E 463 " ideal model delta sigma weight residual 104.50 81.96 22.54 1.90e+00 2.77e-01 1.41e+02 angle pdb=" CB PRO B 463 " pdb=" CG PRO B 463 " pdb=" CD PRO B 463 " ideal model delta sigma weight residual 106.10 132.31 -26.21 3.20e+00 9.77e-02 6.71e+01 ... (remaining 45319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 18282 17.81 - 35.63: 1878 35.63 - 53.44: 240 53.44 - 71.25: 56 71.25 - 89.06: 20 Dihedral angle restraints: 20476 sinusoidal: 8586 harmonic: 11890 Sorted by residual: dihedral pdb=" CA GLN A 541 " pdb=" C GLN A 541 " pdb=" N PRO A 542 " pdb=" CA PRO A 542 " ideal model delta harmonic sigma weight residual -180.00 -150.20 -29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA GLN D 541 " pdb=" C GLN D 541 " pdb=" N PRO D 542 " pdb=" CA PRO D 542 " ideal model delta harmonic sigma weight residual -180.00 -150.24 -29.76 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ILE B1102 " pdb=" C ILE B1102 " pdb=" N PRO B1103 " pdb=" CA PRO B1103 " ideal model delta harmonic sigma weight residual 180.00 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 20473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3984 0.058 - 0.115: 929 0.115 - 0.173: 93 0.173 - 0.231: 14 0.231 - 0.288: 4 Chirality restraints: 5024 Sorted by residual: chirality pdb=" CG LEU E1338 " pdb=" CB LEU E1338 " pdb=" CD1 LEU E1338 " pdb=" CD2 LEU E1338 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.08e+00 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 -2.30 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE C 137 " pdb=" CA ILE C 137 " pdb=" CG1 ILE C 137 " pdb=" CG2 ILE C 137 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 5021 not shown) Planarity restraints: 5796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 462 " -0.059 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO B 463 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 462 " 0.059 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO E 463 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 463 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 463 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER E1530 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C SER E1530 " -0.046 2.00e-02 2.50e+03 pdb=" O SER E1530 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN E1531 " 0.015 2.00e-02 2.50e+03 ... (remaining 5793 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 781 2.63 - 3.20: 35745 3.20 - 3.77: 57386 3.77 - 4.33: 79651 4.33 - 4.90: 117369 Nonbonded interactions: 290932 Sorted by model distance: nonbonded pdb=" O LEU B1120 " pdb=" OG1 THR B1124 " model vdw 2.063 3.040 nonbonded pdb=" O LEU E1120 " pdb=" OG1 THR E1124 " model vdw 2.063 3.040 nonbonded pdb=" ND2 ASN A 670 " pdb=" O ASP A 676 " model vdw 2.064 3.120 nonbonded pdb=" ND2 ASN D 670 " pdb=" O ASP D 676 " model vdw 2.065 3.120 nonbonded pdb=" O ASP B 441 " pdb=" OG1 THR B 629 " model vdw 2.070 3.040 ... (remaining 290927 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'E' } 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.240 Set scattering table: 0.370 Process input model: 72.290 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.140 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.007 0.474 33556 Z= 0.307 Angle : 0.885 26.206 45324 Z= 0.488 Chirality : 0.047 0.288 5024 Planarity : 0.005 0.082 5796 Dihedral : 14.031 89.063 12780 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 36.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.05 % Allowed : 0.71 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 4022 helix: -0.40 (0.11), residues: 1956 sheet: -1.29 (0.23), residues: 468 loop : -1.40 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 575 HIS 0.009 0.002 HIS E 949 PHE 0.029 0.002 PHE F 90 TYR 0.021 0.002 TYR B1328 ARG 0.010 0.001 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.18378 ( 1685) hydrogen bonds : angle 7.40341 ( 4893) covalent geometry : bond 0.00679 (33556) covalent geometry : angle 0.88517 (45324) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 4.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.8989 (mmp) cc_final: 0.8673 (mmm) REVERT: B 1 MET cc_start: 0.4082 (mmp) cc_final: 0.2905 (tpp) REVERT: B 12 TYR cc_start: 0.7932 (m-80) cc_final: 0.7591 (m-80) REVERT: B 115 ARG cc_start: 0.9116 (mmm-85) cc_final: 0.8822 (mmm-85) REVERT: B 120 MET cc_start: 0.9008 (mmp) cc_final: 0.8539 (mmm) REVERT: B 306 MET cc_start: 0.1899 (mmm) cc_final: 0.0399 (ttm) REVERT: B 431 MET cc_start: 0.4701 (mmm) cc_final: 0.4467 (mmm) REVERT: B 802 MET cc_start: 0.7482 (ppp) cc_final: 0.7013 (ppp) REVERT: B 914 ASP cc_start: 0.8950 (t70) cc_final: 0.8668 (t0) REVERT: B 1011 MET cc_start: 0.8477 (tpp) cc_final: 0.8253 (tpp) REVERT: B 1482 MET cc_start: 0.7652 (mmm) cc_final: 0.6867 (mmm) REVERT: B 1522 MET cc_start: 0.9248 (tpt) cc_final: 0.8534 (tpp) REVERT: D 692 MET cc_start: 0.9092 (mmp) cc_final: 0.8812 (mmm) REVERT: E 120 MET cc_start: 0.9203 (mmp) cc_final: 0.8751 (mmm) REVERT: E 800 MET cc_start: 0.9191 (mpp) cc_final: 0.8820 (ptt) REVERT: E 802 MET cc_start: 0.7357 (ppp) cc_final: 0.6861 (ppp) REVERT: E 1435 MET cc_start: 0.8122 (tpt) cc_final: 0.7879 (tpt) REVERT: E 1522 MET cc_start: 0.9201 (tpt) cc_final: 0.8659 (tpp) REVERT: E 1560 MET cc_start: 0.6955 (ppp) cc_final: 0.6436 (ppp) REVERT: E 1597 MET cc_start: 0.8827 (tpp) cc_final: 0.8581 (ttm) outliers start: 2 outliers final: 0 residues processed: 186 average time/residue: 0.4524 time to fit residues: 140.4081 Evaluate side-chains 145 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 9.9990 chunk 303 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 313 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 233 optimal weight: 6.9990 chunk 363 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 ASN B1035 GLN B1203 ASN B1267 HIS B1293 GLN ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 HIS ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1014 ASN E1035 GLN E1203 ASN E1267 HIS E1293 GLN ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.052659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.031397 restraints weight = 311152.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.031477 restraints weight = 199274.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.032063 restraints weight = 147150.006| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33556 Z= 0.162 Angle : 0.680 19.184 45324 Z= 0.353 Chirality : 0.045 0.204 5024 Planarity : 0.005 0.062 5796 Dihedral : 5.487 80.916 4394 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.27 % Allowed : 6.31 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 4022 helix: 0.10 (0.11), residues: 2016 sheet: -1.22 (0.23), residues: 484 loop : -1.05 (0.17), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 102 HIS 0.007 0.001 HIS E 949 PHE 0.018 0.002 PHE E 184 TYR 0.024 0.002 TYR B1289 ARG 0.018 0.001 ARG E 935 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 1685) hydrogen bonds : angle 5.98330 ( 4893) covalent geometry : bond 0.00342 (33556) covalent geometry : angle 0.68015 (45324) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 ARG cc_start: 0.8461 (mmp80) cc_final: 0.8077 (mmp80) REVERT: A 692 MET cc_start: 0.9026 (mmp) cc_final: 0.8706 (mmm) REVERT: A 720 TYR cc_start: 0.6453 (m-80) cc_final: 0.5621 (m-10) REVERT: B 1 MET cc_start: 0.4313 (mmp) cc_final: 0.4021 (tpp) REVERT: B 12 TYR cc_start: 0.8093 (m-80) cc_final: 0.7762 (m-80) REVERT: B 120 MET cc_start: 0.9076 (mmp) cc_final: 0.8539 (mmm) REVERT: B 306 MET cc_start: 0.2361 (mmm) cc_final: 0.1399 (ttt) REVERT: B 431 MET cc_start: 0.5426 (mmm) cc_final: 0.5133 (mmm) REVERT: B 1011 MET cc_start: 0.8619 (tpp) cc_final: 0.8258 (tpp) REVERT: B 1035 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: B 1243 TYR cc_start: 0.8771 (m-80) cc_final: 0.8556 (m-80) REVERT: B 1313 MET cc_start: 0.7441 (tmm) cc_final: 0.7132 (tmm) REVERT: B 1522 MET cc_start: 0.9278 (tpt) cc_final: 0.8487 (tpp) REVERT: D 692 MET cc_start: 0.9110 (mmp) cc_final: 0.8769 (mmt) REVERT: E 120 MET cc_start: 0.9245 (mmp) cc_final: 0.8818 (mmm) REVERT: E 800 MET cc_start: 0.9086 (mpp) cc_final: 0.8752 (ptt) REVERT: E 802 MET cc_start: 0.7015 (ppp) cc_final: 0.6604 (ppp) REVERT: E 1009 MET cc_start: 0.9051 (mmm) cc_final: 0.8768 (mmt) REVERT: E 1035 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: E 1243 TYR cc_start: 0.8960 (m-80) cc_final: 0.8634 (m-80) REVERT: E 1435 MET cc_start: 0.8260 (tpt) cc_final: 0.7993 (tpt) REVERT: E 1522 MET cc_start: 0.9319 (tpt) cc_final: 0.8679 (tpp) REVERT: E 1560 MET cc_start: 0.6747 (ppp) cc_final: 0.6272 (ppp) REVERT: E 1597 MET cc_start: 0.8840 (tpp) cc_final: 0.8591 (ttm) REVERT: F 1 MET cc_start: 0.6277 (tpt) cc_final: 0.6073 (tpt) REVERT: F 45 MET cc_start: 0.8573 (tpp) cc_final: 0.8300 (tpt) outliers start: 10 outliers final: 1 residues processed: 201 average time/residue: 0.4153 time to fit residues: 142.1596 Evaluate side-chains 154 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 386 optimal weight: 6.9990 chunk 306 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 116 optimal weight: 8.9990 chunk 374 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 316 optimal weight: 1.9990 chunk 387 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.051166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.030143 restraints weight = 274917.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.030633 restraints weight = 187999.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.031059 restraints weight = 144507.376| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33556 Z= 0.204 Angle : 0.687 14.633 45324 Z= 0.358 Chirality : 0.044 0.224 5024 Planarity : 0.005 0.059 5796 Dihedral : 5.489 80.421 4394 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 4022 helix: 0.04 (0.11), residues: 2016 sheet: -1.34 (0.23), residues: 484 loop : -1.23 (0.17), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 102 HIS 0.007 0.002 HIS D 601 PHE 0.017 0.002 PHE E 184 TYR 0.021 0.002 TYR B1388 ARG 0.009 0.001 ARG E 935 Details of bonding type rmsd hydrogen bonds : bond 0.04736 ( 1685) hydrogen bonds : angle 5.88325 ( 4893) covalent geometry : bond 0.00425 (33556) covalent geometry : angle 0.68720 (45324) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 4.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 ARG cc_start: 0.8535 (mmp80) cc_final: 0.8058 (mmp80) REVERT: A 692 MET cc_start: 0.9115 (mmp) cc_final: 0.8830 (mmm) REVERT: B 1 MET cc_start: 0.4496 (mmp) cc_final: 0.3711 (tpp) REVERT: B 12 TYR cc_start: 0.8137 (m-80) cc_final: 0.7775 (m-80) REVERT: B 120 MET cc_start: 0.9119 (mmp) cc_final: 0.8680 (mmm) REVERT: B 306 MET cc_start: 0.2999 (mmm) cc_final: 0.2763 (mmm) REVERT: B 431 MET cc_start: 0.4830 (mmm) cc_final: 0.4428 (mmm) REVERT: B 1011 MET cc_start: 0.8773 (tpp) cc_final: 0.8380 (tpp) REVERT: B 1313 MET cc_start: 0.7836 (tmm) cc_final: 0.7351 (tmm) REVERT: B 1522 MET cc_start: 0.9287 (tpt) cc_final: 0.8460 (tpp) REVERT: B 1560 MET cc_start: 0.7606 (ptm) cc_final: 0.6919 (ttp) REVERT: C 45 MET cc_start: 0.8261 (tpt) cc_final: 0.8038 (tpt) REVERT: D 692 MET cc_start: 0.9197 (mmp) cc_final: 0.8880 (mmt) REVERT: E 120 MET cc_start: 0.9259 (mmp) cc_final: 0.8915 (mmm) REVERT: E 764 PHE cc_start: 0.9482 (m-10) cc_final: 0.9273 (m-10) REVERT: E 800 MET cc_start: 0.9157 (mpp) cc_final: 0.8823 (ptt) REVERT: E 802 MET cc_start: 0.6929 (ppp) cc_final: 0.6446 (ppp) REVERT: E 1313 MET cc_start: 0.8177 (tmm) cc_final: 0.7824 (tmm) REVERT: E 1435 MET cc_start: 0.8337 (tpt) cc_final: 0.8016 (tpt) REVERT: E 1522 MET cc_start: 0.9368 (tpt) cc_final: 0.8640 (tpt) REVERT: E 1560 MET cc_start: 0.6857 (ppp) cc_final: 0.6498 (ppp) REVERT: E 1597 MET cc_start: 0.8918 (tpp) cc_final: 0.8503 (ttm) REVERT: F 1 MET cc_start: 0.6224 (tpt) cc_final: 0.5985 (tpt) outliers start: 3 outliers final: 0 residues processed: 175 average time/residue: 0.4268 time to fit residues: 127.4818 Evaluate side-chains 146 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 341 optimal weight: 2.9990 chunk 296 optimal weight: 0.9980 chunk 378 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 130 GLN B 414 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1035 GLN B1097 HIS ** B1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 788 ASN ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1035 GLN E1097 HIS F 2 GLN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.052901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.033754 restraints weight = 352928.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.034143 restraints weight = 222201.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.034587 restraints weight = 163230.656| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33556 Z= 0.149 Angle : 0.651 16.215 45324 Z= 0.334 Chirality : 0.043 0.206 5024 Planarity : 0.005 0.060 5796 Dihedral : 5.369 80.621 4394 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.19 % Allowed : 4.75 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4022 helix: 0.24 (0.12), residues: 2012 sheet: -1.17 (0.23), residues: 470 loop : -1.20 (0.17), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 102 HIS 0.016 0.001 HIS B 187 PHE 0.030 0.001 PHE B1308 TYR 0.016 0.002 TYR B1388 ARG 0.014 0.001 ARG B1088 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 1685) hydrogen bonds : angle 5.59098 ( 4893) covalent geometry : bond 0.00314 (33556) covalent geometry : angle 0.65102 (45324) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 3.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.9042 (mmp) cc_final: 0.8725 (mmm) REVERT: B 1 MET cc_start: 0.4270 (mmp) cc_final: 0.3491 (tpp) REVERT: B 12 TYR cc_start: 0.7877 (m-80) cc_final: 0.7467 (m-10) REVERT: B 97 GLU cc_start: 0.8795 (pp20) cc_final: 0.8160 (pp20) REVERT: B 98 TRP cc_start: 0.9177 (m100) cc_final: 0.8965 (m100) REVERT: B 120 MET cc_start: 0.9059 (mmp) cc_final: 0.8581 (mmm) REVERT: B 431 MET cc_start: 0.5744 (mmm) cc_final: 0.5522 (mmm) REVERT: B 1011 MET cc_start: 0.8718 (tpp) cc_final: 0.8307 (tpp) REVERT: B 1033 MET cc_start: 0.6622 (tpt) cc_final: 0.6347 (mmm) REVERT: B 1243 TYR cc_start: 0.8632 (m-80) cc_final: 0.8378 (m-80) REVERT: B 1313 MET cc_start: 0.8026 (tmm) cc_final: 0.7657 (tmm) REVERT: B 1522 MET cc_start: 0.9246 (tpt) cc_final: 0.8304 (tpt) REVERT: B 1560 MET cc_start: 0.7259 (ptm) cc_final: 0.6592 (ttp) REVERT: D 692 MET cc_start: 0.9120 (mmp) cc_final: 0.8795 (mmt) REVERT: E 120 MET cc_start: 0.9245 (mmp) cc_final: 0.8931 (mmm) REVERT: E 800 MET cc_start: 0.9164 (mpp) cc_final: 0.8862 (ptt) REVERT: E 802 MET cc_start: 0.6809 (ppp) cc_final: 0.6270 (ppp) REVERT: E 1009 MET cc_start: 0.9156 (mmp) cc_final: 0.8907 (mmm) REVERT: E 1033 MET cc_start: 0.6995 (tpt) cc_final: 0.6713 (tmm) REVERT: E 1035 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: E 1313 MET cc_start: 0.8097 (tmm) cc_final: 0.7624 (tmm) REVERT: E 1435 MET cc_start: 0.8286 (tpt) cc_final: 0.8045 (tpt) REVERT: E 1522 MET cc_start: 0.9346 (tpt) cc_final: 0.8599 (tpt) REVERT: E 1560 MET cc_start: 0.6621 (ppp) cc_final: 0.6314 (ppp) REVERT: E 1597 MET cc_start: 0.8881 (tpp) cc_final: 0.8412 (ttm) REVERT: F 1 MET cc_start: 0.6066 (tpt) cc_final: 0.5825 (tpt) REVERT: F 45 MET cc_start: 0.8190 (tpt) cc_final: 0.7848 (tpt) outliers start: 7 outliers final: 0 residues processed: 185 average time/residue: 0.4197 time to fit residues: 131.2159 Evaluate side-chains 148 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 3.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 343 optimal weight: 5.9990 chunk 301 optimal weight: 0.9980 chunk 394 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 246 optimal weight: 0.0570 chunk 157 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 overall best weight: 2.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.052690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.033216 restraints weight = 352150.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.033892 restraints weight = 223179.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.034335 restraints weight = 168296.518| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33556 Z= 0.161 Angle : 0.655 17.333 45324 Z= 0.336 Chirality : 0.043 0.202 5024 Planarity : 0.005 0.059 5796 Dihedral : 5.329 80.459 4394 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4022 helix: 0.27 (0.11), residues: 2008 sheet: -1.08 (0.23), residues: 490 loop : -1.21 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 56 HIS 0.015 0.001 HIS B 187 PHE 0.019 0.002 PHE E 184 TYR 0.017 0.002 TYR B1388 ARG 0.010 0.001 ARG E1627 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 1685) hydrogen bonds : angle 5.57077 ( 4893) covalent geometry : bond 0.00341 (33556) covalent geometry : angle 0.65454 (45324) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 4.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.9073 (mmp) cc_final: 0.8761 (mmm) REVERT: B 1 MET cc_start: 0.4307 (mmp) cc_final: 0.3640 (tpp) REVERT: B 12 TYR cc_start: 0.7889 (m-80) cc_final: 0.7579 (m-80) REVERT: B 115 ARG cc_start: 0.9053 (mmm-85) cc_final: 0.8716 (mmm-85) REVERT: B 120 MET cc_start: 0.9133 (mmp) cc_final: 0.8643 (mmm) REVERT: B 306 MET cc_start: 0.3248 (mmm) cc_final: 0.2303 (ttt) REVERT: B 1009 MET cc_start: 0.9002 (mmp) cc_final: 0.8593 (mmm) REVERT: B 1011 MET cc_start: 0.8798 (tpp) cc_final: 0.8363 (tpp) REVERT: B 1243 TYR cc_start: 0.8848 (m-80) cc_final: 0.8600 (m-80) REVERT: B 1313 MET cc_start: 0.7876 (tmm) cc_final: 0.7416 (tmm) REVERT: B 1522 MET cc_start: 0.9250 (tpt) cc_final: 0.8444 (tpp) REVERT: B 1560 MET cc_start: 0.7270 (ptm) cc_final: 0.6525 (ttp) REVERT: C 45 MET cc_start: 0.8195 (tpt) cc_final: 0.7984 (tpt) REVERT: D 692 MET cc_start: 0.9155 (mmp) cc_final: 0.8834 (mmt) REVERT: E 120 MET cc_start: 0.9240 (mmp) cc_final: 0.8915 (mmm) REVERT: E 800 MET cc_start: 0.9169 (mpp) cc_final: 0.8822 (ptt) REVERT: E 802 MET cc_start: 0.7068 (ppp) cc_final: 0.6570 (ppp) REVERT: E 1011 MET cc_start: 0.8650 (tpp) cc_final: 0.8419 (tpt) REVERT: E 1243 TYR cc_start: 0.9176 (m-80) cc_final: 0.8394 (m-80) REVERT: E 1313 MET cc_start: 0.8019 (tmm) cc_final: 0.7709 (tmm) REVERT: E 1435 MET cc_start: 0.8290 (tpt) cc_final: 0.8029 (tpt) REVERT: E 1522 MET cc_start: 0.9307 (tpt) cc_final: 0.8674 (tpp) REVERT: E 1560 MET cc_start: 0.6641 (ppp) cc_final: 0.6335 (ppp) REVERT: E 1597 MET cc_start: 0.8712 (tpp) cc_final: 0.8365 (ttm) REVERT: F 1 MET cc_start: 0.6045 (tpt) cc_final: 0.5829 (tpt) outliers start: 2 outliers final: 0 residues processed: 173 average time/residue: 0.4316 time to fit residues: 125.9110 Evaluate side-chains 140 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 0.0670 chunk 167 optimal weight: 0.9990 chunk 316 optimal weight: 7.9990 chunk 303 optimal weight: 0.4980 chunk 358 optimal weight: 10.0000 chunk 338 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 397 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 264 optimal weight: 30.0000 overall best weight: 0.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 788 ASN ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.053008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.031935 restraints weight = 312071.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.032134 restraints weight = 197326.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.032701 restraints weight = 144034.591| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33556 Z= 0.123 Angle : 0.643 18.327 45324 Z= 0.325 Chirality : 0.043 0.184 5024 Planarity : 0.004 0.069 5796 Dihedral : 5.179 81.012 4394 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4022 helix: 0.46 (0.12), residues: 2000 sheet: -1.01 (0.22), residues: 498 loop : -1.18 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 102 HIS 0.008 0.001 HIS B 187 PHE 0.016 0.001 PHE E 184 TYR 0.016 0.001 TYR B1288 ARG 0.012 0.001 ARG E 935 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 1685) hydrogen bonds : angle 5.35243 ( 4893) covalent geometry : bond 0.00266 (33556) covalent geometry : angle 0.64347 (45324) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.9064 (mmp) cc_final: 0.8720 (mmm) REVERT: B 1 MET cc_start: 0.4336 (mmp) cc_final: 0.3669 (tpp) REVERT: B 12 TYR cc_start: 0.7705 (m-80) cc_final: 0.7383 (m-80) REVERT: B 115 ARG cc_start: 0.9118 (mmm-85) cc_final: 0.8791 (mmm-85) REVERT: B 120 MET cc_start: 0.9148 (mmp) cc_final: 0.8662 (mmm) REVERT: B 1011 MET cc_start: 0.8602 (tpp) cc_final: 0.8268 (tpp) REVERT: B 1038 PHE cc_start: 0.8007 (p90) cc_final: 0.7674 (p90) REVERT: B 1054 LEU cc_start: 0.9371 (tp) cc_final: 0.9140 (mt) REVERT: B 1313 MET cc_start: 0.7898 (tmm) cc_final: 0.7418 (tmm) REVERT: B 1435 MET cc_start: 0.8392 (tpt) cc_final: 0.7952 (tpt) REVERT: B 1522 MET cc_start: 0.9211 (tpt) cc_final: 0.8500 (tpp) REVERT: B 1560 MET cc_start: 0.7081 (ptm) cc_final: 0.6414 (ttp) REVERT: D 692 MET cc_start: 0.9137 (mmp) cc_final: 0.8808 (mmt) REVERT: E 120 MET cc_start: 0.9272 (mmp) cc_final: 0.8924 (mmm) REVERT: E 800 MET cc_start: 0.9184 (mpp) cc_final: 0.8861 (ptt) REVERT: E 802 MET cc_start: 0.7171 (ppp) cc_final: 0.6676 (ppp) REVERT: E 860 MET cc_start: 0.8584 (ptp) cc_final: 0.8349 (ptp) REVERT: E 906 LEU cc_start: 0.9689 (tp) cc_final: 0.9384 (tt) REVERT: E 929 MET cc_start: 0.8701 (ttm) cc_final: 0.8419 (ttm) REVERT: E 1243 TYR cc_start: 0.9156 (m-80) cc_final: 0.8407 (m-80) REVERT: E 1313 MET cc_start: 0.8042 (tmm) cc_final: 0.7709 (tmm) REVERT: E 1522 MET cc_start: 0.9277 (tpt) cc_final: 0.8543 (tpp) REVERT: E 1560 MET cc_start: 0.6608 (ppp) cc_final: 0.6118 (ppp) REVERT: E 1597 MET cc_start: 0.8719 (tpp) cc_final: 0.8288 (ttm) REVERT: F 45 MET cc_start: 0.8127 (tpt) cc_final: 0.7925 (tpt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.4186 time to fit residues: 127.5562 Evaluate side-chains 149 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 258 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 228 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 325 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 329 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 944 ASN ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1565 ASN ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** 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 = 0.3660 r_free = 0.3660 target = 0.052281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.031177 restraints weight = 309979.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.031296 restraints weight = 202209.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.031887 restraints weight = 147392.109| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 33556 Z= 0.146 Angle : 0.649 19.174 45324 Z= 0.332 Chirality : 0.043 0.188 5024 Planarity : 0.005 0.058 5796 Dihedral : 5.195 80.526 4394 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4022 helix: 0.49 (0.12), residues: 1996 sheet: -1.04 (0.22), residues: 492 loop : -1.21 (0.17), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 56 HIS 0.010 0.001 HIS B 187 PHE 0.024 0.001 PHE B1064 TYR 0.019 0.001 TYR B1289 ARG 0.011 0.001 ARG E1627 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 1685) hydrogen bonds : angle 5.42235 ( 4893) covalent geometry : bond 0.00313 (33556) covalent geometry : angle 0.64896 (45324) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 4.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.9077 (mmp) cc_final: 0.8733 (mmm) REVERT: B 1 MET cc_start: 0.4289 (mmp) cc_final: 0.3637 (tpp) REVERT: B 12 TYR cc_start: 0.7636 (m-80) cc_final: 0.7306 (m-80) REVERT: B 115 ARG cc_start: 0.9076 (mmm-85) cc_final: 0.8804 (mmm-85) REVERT: B 120 MET cc_start: 0.9133 (mmp) cc_final: 0.8628 (mmm) REVERT: B 306 MET cc_start: 0.2873 (mmm) cc_final: 0.1400 (ttt) REVERT: B 964 MET cc_start: 0.7934 (tpt) cc_final: 0.7664 (tpp) REVERT: B 1009 MET cc_start: 0.8973 (mmp) cc_final: 0.8676 (mmm) REVERT: B 1038 PHE cc_start: 0.7902 (p90) cc_final: 0.7651 (p90) REVERT: B 1079 MET cc_start: 0.8148 (mtt) cc_final: 0.7809 (mtt) REVERT: B 1313 MET cc_start: 0.7306 (tmm) cc_final: 0.7069 (tmm) REVERT: B 1522 MET cc_start: 0.9200 (tpt) cc_final: 0.8508 (tpp) REVERT: B 1560 MET cc_start: 0.7111 (ptm) cc_final: 0.6307 (ttp) REVERT: D 692 MET cc_start: 0.9132 (mmp) cc_final: 0.8809 (mmt) REVERT: E 120 MET cc_start: 0.9238 (mmp) cc_final: 0.8886 (mmm) REVERT: E 800 MET cc_start: 0.9220 (mpp) cc_final: 0.8915 (ptt) REVERT: E 802 MET cc_start: 0.7209 (ppp) cc_final: 0.6704 (ppp) REVERT: E 1158 GLU cc_start: 0.8793 (mp0) cc_final: 0.8464 (mp0) REVERT: E 1243 TYR cc_start: 0.9091 (m-80) cc_final: 0.8367 (m-80) REVERT: E 1313 MET cc_start: 0.8142 (tmm) cc_final: 0.7786 (tmm) REVERT: E 1522 MET cc_start: 0.9341 (tpt) cc_final: 0.8620 (tpp) REVERT: E 1560 MET cc_start: 0.6670 (ppp) cc_final: 0.6136 (ppp) REVERT: E 1597 MET cc_start: 0.8739 (tpp) cc_final: 0.8317 (ttm) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.4435 time to fit residues: 131.0799 Evaluate side-chains 141 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 117 optimal weight: 1.9990 chunk 206 optimal weight: 0.0370 chunk 109 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 334 optimal weight: 0.8980 chunk 357 optimal weight: 7.9990 chunk 322 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 293 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 556 ASN ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 944 ASN ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.053121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.032207 restraints weight = 312376.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.032389 restraints weight = 196432.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.032851 restraints weight = 142096.030| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 33556 Z= 0.123 Angle : 0.657 18.311 45324 Z= 0.331 Chirality : 0.044 0.229 5024 Planarity : 0.005 0.094 5796 Dihedral : 5.102 80.815 4394 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.13), residues: 4022 helix: 0.63 (0.12), residues: 1994 sheet: -0.93 (0.22), residues: 492 loop : -1.25 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 56 HIS 0.005 0.001 HIS E 949 PHE 0.020 0.001 PHE E 184 TYR 0.019 0.001 TYR B 969 ARG 0.016 0.001 ARG B1627 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 1685) hydrogen bonds : angle 5.30503 ( 4893) covalent geometry : bond 0.00265 (33556) covalent geometry : angle 0.65738 (45324) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 LYS cc_start: 0.9349 (pptt) cc_final: 0.8927 (ttmt) REVERT: A 677 MET cc_start: 0.7783 (mmp) cc_final: 0.6954 (mmm) REVERT: A 692 MET cc_start: 0.9071 (mmp) cc_final: 0.8703 (mmm) REVERT: B 1 MET cc_start: 0.5439 (mmp) cc_final: 0.4641 (tpp) REVERT: B 12 TYR cc_start: 0.7562 (m-80) cc_final: 0.7215 (m-80) REVERT: B 115 ARG cc_start: 0.9118 (mmm-85) cc_final: 0.8815 (mmm-85) REVERT: B 120 MET cc_start: 0.9178 (mmp) cc_final: 0.8684 (mmm) REVERT: B 306 MET cc_start: 0.2714 (mmm) cc_final: 0.1377 (ttt) REVERT: B 681 MET cc_start: 0.6352 (ptp) cc_final: 0.5401 (ppp) REVERT: B 964 MET cc_start: 0.7700 (tpt) cc_final: 0.7128 (tpt) REVERT: B 1009 MET cc_start: 0.9097 (mmp) cc_final: 0.8886 (mmm) REVERT: B 1011 MET cc_start: 0.8399 (tpp) cc_final: 0.8098 (tpp) REVERT: B 1038 PHE cc_start: 0.7936 (p90) cc_final: 0.7663 (p90) REVERT: B 1313 MET cc_start: 0.7016 (tmm) cc_final: 0.6801 (tmm) REVERT: B 1522 MET cc_start: 0.9171 (tpt) cc_final: 0.8450 (tpp) REVERT: B 1560 MET cc_start: 0.7012 (ptm) cc_final: 0.6496 (ttp) REVERT: D 692 MET cc_start: 0.9129 (mmp) cc_final: 0.8827 (mmm) REVERT: E 120 MET cc_start: 0.9282 (mmp) cc_final: 0.8857 (mmt) REVERT: E 800 MET cc_start: 0.9238 (mpp) cc_final: 0.8929 (ptt) REVERT: E 961 LEU cc_start: 0.9626 (mt) cc_final: 0.9322 (mp) REVERT: E 1009 MET cc_start: 0.9069 (mmp) cc_final: 0.8842 (mmm) REVERT: E 1231 TYR cc_start: 0.8281 (m-10) cc_final: 0.8021 (m-10) REVERT: E 1243 TYR cc_start: 0.9177 (m-80) cc_final: 0.8568 (m-80) REVERT: E 1313 MET cc_start: 0.8066 (tmm) cc_final: 0.7636 (tmm) REVERT: E 1522 MET cc_start: 0.9353 (tpt) cc_final: 0.8607 (tpp) REVERT: E 1560 MET cc_start: 0.6362 (ppp) cc_final: 0.5969 (ppp) REVERT: E 1597 MET cc_start: 0.8743 (tpp) cc_final: 0.8366 (ttm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.4193 time to fit residues: 132.0216 Evaluate side-chains 152 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 24 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 285 optimal weight: 20.0000 chunk 291 optimal weight: 0.0770 chunk 357 optimal weight: 2.9990 chunk 364 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 367 optimal weight: 7.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 944 ASN ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.051433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.030574 restraints weight = 273617.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.031164 restraints weight = 183667.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.031603 restraints weight = 141977.713| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 33556 Z= 0.168 Angle : 0.683 17.781 45324 Z= 0.351 Chirality : 0.044 0.229 5024 Planarity : 0.005 0.085 5796 Dihedral : 5.171 79.879 4394 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 4022 helix: 0.53 (0.12), residues: 1990 sheet: -0.93 (0.22), residues: 492 loop : -1.25 (0.17), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 102 HIS 0.008 0.001 HIS B 187 PHE 0.026 0.002 PHE E1064 TYR 0.047 0.002 TYR B1328 ARG 0.010 0.001 ARG B 935 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 1685) hydrogen bonds : angle 5.46385 ( 4893) covalent geometry : bond 0.00360 (33556) covalent geometry : angle 0.68295 (45324) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 3.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 LYS cc_start: 0.9318 (pptt) cc_final: 0.8903 (ttmt) REVERT: A 692 MET cc_start: 0.9143 (mmp) cc_final: 0.8811 (mmm) REVERT: B 1 MET cc_start: 0.5522 (mmp) cc_final: 0.4682 (tpp) REVERT: B 12 TYR cc_start: 0.7838 (m-80) cc_final: 0.7516 (m-80) REVERT: B 115 ARG cc_start: 0.9171 (mmm-85) cc_final: 0.8943 (mmm-85) REVERT: B 120 MET cc_start: 0.9178 (mmp) cc_final: 0.8745 (mmm) REVERT: B 1009 MET cc_start: 0.9193 (mmp) cc_final: 0.8770 (mmm) REVERT: B 1038 PHE cc_start: 0.7606 (p90) cc_final: 0.7213 (p90) REVERT: B 1158 GLU cc_start: 0.8906 (mp0) cc_final: 0.8496 (mp0) REVERT: B 1313 MET cc_start: 0.7231 (tmm) cc_final: 0.6980 (tmm) REVERT: B 1435 MET cc_start: 0.8572 (tpt) cc_final: 0.8055 (tpt) REVERT: B 1522 MET cc_start: 0.9270 (tpt) cc_final: 0.8574 (tpp) REVERT: B 1560 MET cc_start: 0.7371 (ptm) cc_final: 0.6639 (ttp) REVERT: C 91 GLU cc_start: 0.9308 (mp0) cc_final: 0.9098 (mp0) REVERT: D 549 LYS cc_start: 0.9504 (pttm) cc_final: 0.9224 (mmtm) REVERT: D 569 ARG cc_start: 0.3224 (mmt180) cc_final: 0.2860 (ptp90) REVERT: D 677 MET cc_start: 0.7171 (mmp) cc_final: 0.6102 (mmp) REVERT: D 692 MET cc_start: 0.9176 (mmp) cc_final: 0.8872 (mmm) REVERT: E 120 MET cc_start: 0.9285 (mmp) cc_final: 0.8893 (mmt) REVERT: E 764 PHE cc_start: 0.9508 (m-80) cc_final: 0.9284 (m-80) REVERT: E 800 MET cc_start: 0.9256 (mpp) cc_final: 0.8936 (ptt) REVERT: E 1009 MET cc_start: 0.9182 (mmp) cc_final: 0.8905 (mmm) REVERT: E 1033 MET cc_start: 0.7164 (mmm) cc_final: 0.6823 (mmm) REVERT: E 1158 GLU cc_start: 0.8972 (mp0) cc_final: 0.8499 (mp0) REVERT: E 1243 TYR cc_start: 0.9206 (m-80) cc_final: 0.8414 (m-80) REVERT: E 1313 MET cc_start: 0.7249 (tmm) cc_final: 0.6891 (tmm) REVERT: E 1522 MET cc_start: 0.9425 (tpt) cc_final: 0.8728 (tpp) REVERT: E 1560 MET cc_start: 0.6541 (ppp) cc_final: 0.6180 (ppp) REVERT: E 1597 MET cc_start: 0.8793 (tpp) cc_final: 0.8461 (ttm) REVERT: F 91 GLU cc_start: 0.9197 (mp0) cc_final: 0.8993 (mp0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.4207 time to fit residues: 125.1537 Evaluate side-chains 149 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 4.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 269 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 154 optimal weight: 0.3980 chunk 371 optimal weight: 0.7980 chunk 226 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 307 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 ASN ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1577 GLN ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.052883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.031974 restraints weight = 312007.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.032045 restraints weight = 202122.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.032618 restraints weight = 148646.323| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 33556 Z= 0.127 Angle : 0.669 18.081 45324 Z= 0.337 Chirality : 0.044 0.230 5024 Planarity : 0.004 0.062 5796 Dihedral : 5.063 80.410 4394 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 4022 helix: 0.61 (0.12), residues: 1992 sheet: -0.84 (0.22), residues: 500 loop : -1.27 (0.17), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 102 HIS 0.005 0.001 HIS E 949 PHE 0.023 0.001 PHE E1064 TYR 0.043 0.001 TYR B1328 ARG 0.008 0.001 ARG B1627 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 1685) hydrogen bonds : angle 5.30371 ( 4893) covalent geometry : bond 0.00277 (33556) covalent geometry : angle 0.66917 (45324) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 3.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 LYS cc_start: 0.9345 (pptt) cc_final: 0.8941 (ttmt) REVERT: A 677 MET cc_start: 0.7791 (mmp) cc_final: 0.6975 (mmp) REVERT: A 692 MET cc_start: 0.9077 (mmp) cc_final: 0.8782 (mmp) REVERT: B 1 MET cc_start: 0.5370 (mmp) cc_final: 0.4581 (tpp) REVERT: B 12 TYR cc_start: 0.7781 (m-80) cc_final: 0.7454 (m-80) REVERT: B 115 ARG cc_start: 0.9129 (mmm-85) cc_final: 0.8872 (mmm-85) REVERT: B 120 MET cc_start: 0.9139 (mmp) cc_final: 0.8681 (mmm) REVERT: B 306 MET cc_start: 0.2253 (mmm) cc_final: 0.0997 (ttt) REVERT: B 681 MET cc_start: 0.6279 (ptp) cc_final: 0.5696 (ppp) REVERT: B 961 LEU cc_start: 0.9594 (mt) cc_final: 0.9241 (mt) REVERT: B 1009 MET cc_start: 0.9110 (mmp) cc_final: 0.8683 (mmm) REVERT: B 1038 PHE cc_start: 0.7598 (p90) cc_final: 0.7209 (p90) REVERT: B 1313 MET cc_start: 0.7226 (tmm) cc_final: 0.6967 (tmm) REVERT: B 1435 MET cc_start: 0.8357 (tpt) cc_final: 0.7930 (tpt) REVERT: B 1522 MET cc_start: 0.9156 (tpt) cc_final: 0.8409 (tpp) REVERT: B 1560 MET cc_start: 0.7011 (ptm) cc_final: 0.6390 (ttp) REVERT: D 549 LYS cc_start: 0.9542 (pttm) cc_final: 0.9235 (mmtm) REVERT: D 569 ARG cc_start: 0.3448 (mmt180) cc_final: 0.3148 (ptp90) REVERT: D 677 MET cc_start: 0.7488 (mmp) cc_final: 0.6716 (mmp) REVERT: D 692 MET cc_start: 0.9097 (mmp) cc_final: 0.8681 (mmt) REVERT: E 120 MET cc_start: 0.9296 (mmp) cc_final: 0.8842 (mmt) REVERT: E 306 MET cc_start: 0.3207 (mmm) cc_final: 0.2661 (mmm) REVERT: E 681 MET cc_start: 0.5735 (ptp) cc_final: 0.4336 (mmt) REVERT: E 764 PHE cc_start: 0.9557 (m-80) cc_final: 0.9327 (m-80) REVERT: E 800 MET cc_start: 0.9150 (mpp) cc_final: 0.8908 (ptt) REVERT: E 960 LEU cc_start: 0.9634 (tt) cc_final: 0.9347 (pp) REVERT: E 961 LEU cc_start: 0.9638 (mt) cc_final: 0.9238 (mt) REVERT: E 964 MET cc_start: 0.8147 (tpt) cc_final: 0.7940 (tpt) REVERT: E 1009 MET cc_start: 0.9083 (mmp) cc_final: 0.8837 (mmm) REVERT: E 1033 MET cc_start: 0.7249 (mmm) cc_final: 0.6940 (mmm) REVERT: E 1158 GLU cc_start: 0.8967 (mp0) cc_final: 0.8468 (mp0) REVERT: E 1212 MET cc_start: 0.8367 (mpp) cc_final: 0.8152 (ppp) REVERT: E 1231 TYR cc_start: 0.8178 (m-10) cc_final: 0.7901 (m-10) REVERT: E 1243 TYR cc_start: 0.9191 (m-80) cc_final: 0.8580 (m-80) REVERT: E 1278 CYS cc_start: 0.7139 (m) cc_final: 0.6596 (t) REVERT: E 1313 MET cc_start: 0.7046 (tmm) cc_final: 0.6724 (tmm) REVERT: E 1435 MET cc_start: 0.8346 (tpt) cc_final: 0.7840 (tpt) REVERT: E 1522 MET cc_start: 0.9368 (tpt) cc_final: 0.8642 (tpp) REVERT: E 1549 MET cc_start: 0.8681 (mmp) cc_final: 0.8461 (mmm) REVERT: E 1560 MET cc_start: 0.6450 (ppp) cc_final: 0.5987 (ppp) REVERT: E 1597 MET cc_start: 0.8709 (tpp) cc_final: 0.8335 (ttm) REVERT: F 91 GLU cc_start: 0.9169 (mp0) cc_final: 0.8938 (mp0) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.4410 time to fit residues: 136.9949 Evaluate side-chains 155 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 173 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 284 optimal weight: 0.5980 chunk 184 optimal weight: 0.0980 chunk 121 optimal weight: 6.9990 chunk 396 optimal weight: 6.9990 chunk 373 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 377 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN E 109 ASN ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.053038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.031816 restraints weight = 303312.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.032088 restraints weight = 189239.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.032649 restraints weight = 137182.860| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 33556 Z= 0.121 Angle : 0.662 17.358 45324 Z= 0.333 Chirality : 0.043 0.219 5024 Planarity : 0.004 0.062 5796 Dihedral : 4.980 80.246 4394 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 4022 helix: 0.69 (0.12), residues: 1996 sheet: -0.73 (0.22), residues: 490 loop : -1.28 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 102 HIS 0.005 0.001 HIS E 949 PHE 0.020 0.001 PHE E1064 TYR 0.039 0.001 TYR B1328 ARG 0.007 0.000 ARG B1627 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 1685) hydrogen bonds : angle 5.20303 ( 4893) covalent geometry : bond 0.00262 (33556) covalent geometry : angle 0.66232 (45324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13324.67 seconds wall clock time: 233 minutes 29.68 seconds (14009.68 seconds total)