Starting phenix.real_space_refine on Tue Aug 26 04:17:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjk_60148/08_2025/8zjk_60148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjk_60148/08_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_60148/08_2025/8zjk_60148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjk_60148/08_2025/8zjk_60148.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjk_60148/08_2025/8zjk_60148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjk_60148/08_2025/8zjk_60148.cif" } resolution = 4.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.17, per 1000 atoms: 0.19 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: 2.73 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.29 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: 6.73 Time building geometry restraints manager: 3.52 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 2.220 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 26.700 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.000 ------------------------------------------------------------------------------- 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 : 36.09 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (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 ARG 0.010 0.001 ARG C 66 TYR 0.021 0.002 TYR B1328 PHE 0.029 0.002 PHE F 90 TRP 0.029 0.003 TRP A 575 HIS 0.009 0.002 HIS E 949 Details of bonding type rmsd covalent geometry : bond 0.00679 (33556) covalent geometry : angle 0.88517 (45324) hydrogen bonds : bond 0.18378 ( 1685) hydrogen bonds : angle 7.40341 ( 4893) *********************** 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 : 1.164 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: 0.1879 time to fit residues: 57.9973 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 : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 587 HIS A 596 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** 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** ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1293 GLN ** 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** E 65 HIS ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** 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** ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1203 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.051787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.032687 restraints weight = 363260.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.033154 restraints weight = 229054.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.033581 restraints weight = 169843.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.033776 restraints weight = 142153.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.034115 restraints weight = 131965.122| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 33556 Z= 0.257 Angle : 0.759 19.202 45324 Z= 0.400 Chirality : 0.047 0.243 5024 Planarity : 0.005 0.062 5796 Dihedral : 5.715 79.367 4394 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.22 % Allowed : 7.56 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.13), residues: 4022 helix: -0.26 (0.11), residues: 2006 sheet: -1.33 (0.23), residues: 484 loop : -1.23 (0.17), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E1390 TYR 0.026 0.002 TYR B1289 PHE 0.019 0.002 PHE C 90 TRP 0.023 0.003 TRP D 575 HIS 0.008 0.002 HIS E1619 Details of bonding type rmsd covalent geometry : bond 0.00528 (33556) covalent geometry : angle 0.75855 (45324) hydrogen bonds : bond 0.05543 ( 1685) hydrogen bonds : angle 6.30881 ( 4893) *********************** 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 181 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 1.032 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: 0.9008 (mmp) cc_final: 0.8711 (mmm) REVERT: B 1 MET cc_start: 0.4040 (mmp) cc_final: 0.3506 (tpp) REVERT: B 12 TYR cc_start: 0.7880 (m-80) cc_final: 0.7502 (m-10) REVERT: B 120 MET cc_start: 0.8951 (mmp) cc_final: 0.8390 (mmm) REVERT: B 431 MET cc_start: 0.5688 (mmm) cc_final: 0.5437 (mmm) REVERT: B 1243 TYR cc_start: 0.8924 (m-80) cc_final: 0.8655 (m-80) REVERT: B 1313 MET cc_start: 0.7529 (tmm) cc_final: 0.7081 (tmm) REVERT: B 1522 MET cc_start: 0.9264 (tpt) cc_final: 0.8487 (tpp) REVERT: D 692 MET cc_start: 0.9084 (mmp) cc_final: 0.8792 (mmt) REVERT: E 120 MET cc_start: 0.9221 (mmp) cc_final: 0.8858 (mmm) REVERT: E 555 MET cc_start: 0.4335 (pmm) cc_final: 0.4114 (tpp) REVERT: E 800 MET cc_start: 0.9120 (mpp) cc_final: 0.8810 (ptt) REVERT: E 802 MET cc_start: 0.6976 (ppp) cc_final: 0.6505 (ppp) REVERT: E 1435 MET cc_start: 0.8351 (tpt) cc_final: 0.8037 (tpt) REVERT: E 1522 MET cc_start: 0.9369 (tpt) cc_final: 0.8695 (tpp) REVERT: E 1560 MET cc_start: 0.6749 (ppp) cc_final: 0.6374 (ppp) REVERT: E 1597 MET cc_start: 0.8816 (tpp) cc_final: 0.8586 (ttm) REVERT: F 1 MET cc_start: 0.6244 (tpt) cc_final: 0.5969 (tpt) outliers start: 8 outliers final: 1 residues processed: 181 average time/residue: 0.1637 time to fit residues: 50.7200 Evaluate side-chains 143 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 226 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 397 optimal weight: 5.9990 chunk 265 optimal weight: 30.0000 chunk 38 optimal weight: 0.9990 chunk 249 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 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 B1048 HIS ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 ASN B1267 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 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** E1014 ASN E1035 GLN E1267 HIS E1636 HIS F 2 GLN ** 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 = 0.3640 r_free = 0.3640 target = 0.052505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.033468 restraints weight = 354511.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.033743 restraints weight = 226058.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.034208 restraints weight = 165270.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.034384 restraints weight = 136723.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.034784 restraints weight = 120043.214| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33556 Z= 0.178 Angle : 0.682 15.648 45324 Z= 0.353 Chirality : 0.044 0.210 5024 Planarity : 0.005 0.063 5796 Dihedral : 5.556 80.540 4394 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.19 % Allowed : 5.52 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.13), residues: 4022 helix: -0.05 (0.11), residues: 2018 sheet: -1.38 (0.23), residues: 484 loop : -1.25 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1390 TYR 0.020 0.002 TYR B1388 PHE 0.033 0.002 PHE B1308 TRP 0.021 0.002 TRP E 102 HIS 0.007 0.001 HIS E 949 Details of bonding type rmsd covalent geometry : bond 0.00376 (33556) covalent geometry : angle 0.68198 (45324) hydrogen bonds : bond 0.04685 ( 1685) hydrogen bonds : angle 5.87458 ( 4893) *********************** 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 186 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 179 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.9051 (mmp) cc_final: 0.8749 (mmm) REVERT: B 1 MET cc_start: 0.4270 (mmp) cc_final: 0.3668 (tpp) REVERT: B 12 TYR cc_start: 0.7907 (m-80) cc_final: 0.7492 (m-10) REVERT: B 120 MET cc_start: 0.9045 (mmp) cc_final: 0.8599 (mmm) REVERT: B 306 MET cc_start: 0.3041 (mmm) cc_final: 0.2014 (ttt) REVERT: B 431 MET cc_start: 0.5684 (mmm) cc_final: 0.5420 (mmm) REVERT: B 1011 MET cc_start: 0.8706 (tpp) cc_final: 0.8289 (tpp) REVERT: B 1035 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: B 1156 ASP cc_start: 0.8578 (t70) cc_final: 0.8376 (t0) REVERT: B 1243 TYR cc_start: 0.8838 (m-80) cc_final: 0.8550 (m-80) REVERT: B 1313 MET cc_start: 0.7975 (tmm) cc_final: 0.7675 (tmm) REVERT: B 1522 MET cc_start: 0.9212 (tpt) cc_final: 0.8355 (tpp) REVERT: D 692 MET cc_start: 0.9120 (mmp) cc_final: 0.8857 (mmm) REVERT: E 120 MET cc_start: 0.9200 (mmp) cc_final: 0.8881 (mmm) REVERT: E 658 MET cc_start: 0.7372 (tmm) cc_final: 0.7165 (tmm) REVERT: E 764 PHE cc_start: 0.9541 (m-10) cc_final: 0.9336 (m-10) REVERT: E 800 MET cc_start: 0.9109 (mpp) cc_final: 0.8799 (ptt) REVERT: E 802 MET cc_start: 0.6923 (ppp) cc_final: 0.6384 (ppp) REVERT: E 1035 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: E 1313 MET cc_start: 0.8125 (tmm) cc_final: 0.7875 (tmm) REVERT: E 1435 MET cc_start: 0.8291 (tpt) cc_final: 0.8020 (tpt) REVERT: E 1522 MET cc_start: 0.9386 (tpt) cc_final: 0.8640 (tpt) REVERT: E 1560 MET cc_start: 0.6646 (ppp) cc_final: 0.6331 (ppp) REVERT: E 1597 MET cc_start: 0.8852 (tpp) cc_final: 0.8425 (ttm) REVERT: F 1 MET cc_start: 0.6087 (tpt) cc_final: 0.5810 (tpt) outliers start: 7 outliers final: 0 residues processed: 186 average time/residue: 0.1855 time to fit residues: 57.4029 Evaluate side-chains 149 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 369 optimal weight: 0.6980 chunk 269 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 317 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 210 optimal weight: 0.6980 chunk 223 optimal weight: 20.0000 chunk 338 optimal weight: 5.9990 chunk 385 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1044 ASN B1097 HIS 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.052994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.033968 restraints weight = 350841.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.034304 restraints weight = 221448.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.034800 restraints weight = 162981.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.034942 restraints weight = 132582.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.035325 restraints weight = 120793.209| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33556 Z= 0.139 Angle : 0.660 16.103 45324 Z= 0.336 Chirality : 0.044 0.187 5024 Planarity : 0.005 0.066 5796 Dihedral : 5.408 80.714 4394 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.16 % Allowed : 3.52 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.13), residues: 4022 helix: 0.23 (0.12), residues: 1996 sheet: -1.30 (0.22), residues: 486 loop : -1.25 (0.17), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1088 TYR 0.024 0.002 TYR E1328 PHE 0.016 0.001 PHE E 184 TRP 0.018 0.002 TRP E 102 HIS 0.006 0.001 HIS B 949 Details of bonding type rmsd covalent geometry : bond 0.00299 (33556) covalent geometry : angle 0.66020 (45324) hydrogen bonds : bond 0.04280 ( 1685) hydrogen bonds : angle 5.64554 ( 4893) *********************** 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 181 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.9046 (mmp) cc_final: 0.8742 (mmm) REVERT: B 1 MET cc_start: 0.4174 (mmp) cc_final: 0.3470 (tpp) REVERT: B 12 TYR cc_start: 0.7800 (m-80) cc_final: 0.7385 (m-10) REVERT: B 120 MET cc_start: 0.9096 (mmp) cc_final: 0.8524 (mmm) REVERT: B 431 MET cc_start: 0.5707 (mmm) cc_final: 0.5473 (mmm) REVERT: B 964 MET cc_start: 0.7997 (tpt) cc_final: 0.7751 (tpp) REVERT: B 1011 MET cc_start: 0.8970 (tpp) cc_final: 0.8525 (tpp) REVERT: B 1156 ASP cc_start: 0.8478 (t70) cc_final: 0.8175 (t0) REVERT: B 1243 TYR cc_start: 0.8890 (m-80) cc_final: 0.8601 (m-80) REVERT: B 1313 MET cc_start: 0.7678 (tmm) cc_final: 0.7262 (tmm) REVERT: B 1522 MET cc_start: 0.9255 (tpt) cc_final: 0.8420 (tpp) REVERT: B 1560 MET cc_start: 0.7623 (ptm) cc_final: 0.7209 (ttp) REVERT: D 692 MET cc_start: 0.9131 (mmp) cc_final: 0.8806 (mmt) REVERT: E 120 MET cc_start: 0.9230 (mmp) cc_final: 0.8942 (mmm) REVERT: E 800 MET cc_start: 0.9148 (mpp) cc_final: 0.8857 (ptt) REVERT: E 802 MET cc_start: 0.6859 (ppp) cc_final: 0.6298 (ppp) REVERT: E 1009 MET cc_start: 0.9059 (mmp) cc_final: 0.8843 (mmm) REVERT: E 1033 MET cc_start: 0.7245 (tpt) cc_final: 0.6245 (tmm) REVERT: E 1035 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: E 1313 MET cc_start: 0.7883 (tmm) cc_final: 0.7474 (tmm) REVERT: E 1435 MET cc_start: 0.8349 (tpt) cc_final: 0.8078 (tpt) REVERT: E 1522 MET cc_start: 0.9400 (tpt) cc_final: 0.8646 (tpt) REVERT: E 1560 MET cc_start: 0.6597 (ppp) cc_final: 0.6299 (ppp) REVERT: E 1597 MET cc_start: 0.8882 (tpp) cc_final: 0.8426 (ttm) REVERT: F 1 MET cc_start: 0.6068 (tpt) cc_final: 0.5802 (tpt) REVERT: F 45 MET cc_start: 0.8072 (tpt) cc_final: 0.7762 (tpt) outliers start: 6 outliers final: 0 residues processed: 181 average time/residue: 0.1770 time to fit residues: 54.1402 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 : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 76 optimal weight: 30.0000 chunk 200 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 391 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 300 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 176 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 350 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** 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 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 924 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.052759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.031784 restraints weight = 316682.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.031939 restraints weight = 201567.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.032523 restraints weight = 146456.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.032901 restraints weight = 116773.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.033021 restraints weight = 105018.686| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33556 Z= 0.131 Angle : 0.641 17.557 45324 Z= 0.324 Chirality : 0.043 0.173 5024 Planarity : 0.004 0.070 5796 Dihedral : 5.288 80.935 4394 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.11 % Allowed : 3.63 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.13), residues: 4022 helix: 0.36 (0.12), residues: 2006 sheet: -1.18 (0.22), residues: 504 loop : -1.20 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E1015 TYR 0.020 0.001 TYR E1328 PHE 0.020 0.001 PHE E 184 TRP 0.016 0.002 TRP C 56 HIS 0.005 0.001 HIS E 949 Details of bonding type rmsd covalent geometry : bond 0.00282 (33556) covalent geometry : angle 0.64145 (45324) hydrogen bonds : bond 0.04048 ( 1685) hydrogen bonds : angle 5.44917 ( 4893) *********************** 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 172 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 168 time to evaluate : 1.189 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: 0.9066 (mmp) cc_final: 0.8750 (mmm) REVERT: B 1 MET cc_start: 0.4304 (mmp) cc_final: 0.3653 (tpp) REVERT: B 12 TYR cc_start: 0.7816 (m-80) cc_final: 0.7466 (m-80) REVERT: B 115 ARG cc_start: 0.9048 (mmm-85) cc_final: 0.8700 (mmm-85) REVERT: B 120 MET cc_start: 0.9124 (mmp) cc_final: 0.8645 (mmm) REVERT: B 306 MET cc_start: 0.2997 (mmm) cc_final: 0.1556 (ttt) REVERT: B 431 MET cc_start: 0.5778 (mmm) cc_final: 0.5534 (mmm) REVERT: B 964 MET cc_start: 0.8229 (tpt) cc_final: 0.7903 (tpt) REVERT: B 1011 MET cc_start: 0.8675 (tpp) cc_final: 0.8425 (tpp) REVERT: B 1243 TYR cc_start: 0.8807 (m-80) cc_final: 0.8359 (m-80) REVERT: B 1313 MET cc_start: 0.7950 (tmm) cc_final: 0.7519 (tmm) REVERT: B 1522 MET cc_start: 0.9230 (tpt) cc_final: 0.8347 (tpp) REVERT: B 1560 MET cc_start: 0.7481 (ptm) cc_final: 0.7148 (ttp) REVERT: C 45 MET cc_start: 0.8123 (tpt) cc_final: 0.7885 (tpt) REVERT: D 692 MET cc_start: 0.9146 (mmp) cc_final: 0.8820 (mmt) REVERT: E 120 MET cc_start: 0.9238 (mmp) cc_final: 0.8942 (mmm) REVERT: E 800 MET cc_start: 0.9147 (mpp) cc_final: 0.8829 (ptt) REVERT: E 802 MET cc_start: 0.7047 (ppp) cc_final: 0.6510 (ppp) REVERT: E 964 MET cc_start: 0.8542 (tpp) cc_final: 0.8137 (tpp) REVERT: E 1313 MET cc_start: 0.8012 (tmm) cc_final: 0.7558 (tmm) REVERT: E 1435 MET cc_start: 0.8340 (tpt) cc_final: 0.8049 (tpt) REVERT: E 1522 MET cc_start: 0.9300 (tpt) cc_final: 0.8615 (tpp) REVERT: E 1560 MET cc_start: 0.6570 (ppp) cc_final: 0.6274 (ppp) REVERT: E 1597 MET cc_start: 0.8729 (tpp) cc_final: 0.8238 (ttm) outliers start: 4 outliers final: 0 residues processed: 172 average time/residue: 0.1751 time to fit residues: 50.9446 Evaluate side-chains 143 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 335 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 344 optimal weight: 9.9990 chunk 217 optimal weight: 0.1980 chunk 186 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 334 optimal weight: 0.8980 chunk 313 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 358 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 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** ** 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 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.052546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.031407 restraints weight = 308648.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.031578 restraints weight = 200751.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.032168 restraints weight = 146162.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.032313 restraints weight = 118169.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.032705 restraints weight = 105876.726| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33556 Z= 0.139 Angle : 0.649 18.247 45324 Z= 0.329 Chirality : 0.043 0.212 5024 Planarity : 0.005 0.076 5796 Dihedral : 5.215 80.968 4394 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.13), residues: 4022 helix: 0.42 (0.12), residues: 2002 sheet: -1.05 (0.22), residues: 494 loop : -1.19 (0.17), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1627 TYR 0.019 0.001 TYR E1243 PHE 0.018 0.001 PHE B1064 TRP 0.016 0.002 TRP E 102 HIS 0.005 0.001 HIS B 949 Details of bonding type rmsd covalent geometry : bond 0.00296 (33556) covalent geometry : angle 0.64856 (45324) hydrogen bonds : bond 0.04004 ( 1685) hydrogen bonds : angle 5.45738 ( 4893) *********************** 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 168 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.952 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: 0.9065 (mmp) cc_final: 0.8737 (mmm) REVERT: B 1 MET cc_start: 0.4325 (mmp) cc_final: 0.3648 (tpp) REVERT: B 12 TYR cc_start: 0.7725 (m-80) cc_final: 0.7402 (m-80) REVERT: B 115 ARG cc_start: 0.9056 (mmm-85) cc_final: 0.8736 (mmm-85) REVERT: B 120 MET cc_start: 0.9120 (mmp) cc_final: 0.8635 (mmm) REVERT: B 431 MET cc_start: 0.5765 (mmm) cc_final: 0.5535 (mmm) REVERT: B 964 MET cc_start: 0.8031 (tpt) cc_final: 0.7548 (tpt) REVERT: B 1009 MET cc_start: 0.8883 (mmt) cc_final: 0.8572 (mmm) REVERT: B 1011 MET cc_start: 0.8707 (tpp) cc_final: 0.8354 (tpp) REVERT: B 1038 PHE cc_start: 0.7846 (p90) cc_final: 0.7521 (p90) REVERT: B 1243 TYR cc_start: 0.8900 (m-80) cc_final: 0.8475 (m-80) REVERT: B 1313 MET cc_start: 0.7869 (tmm) cc_final: 0.7580 (tmm) REVERT: B 1435 MET cc_start: 0.8528 (tpt) cc_final: 0.8316 (tpt) REVERT: B 1522 MET cc_start: 0.9230 (tpt) cc_final: 0.8536 (tpp) REVERT: B 1560 MET cc_start: 0.7439 (ptm) cc_final: 0.7063 (ttp) REVERT: D 692 MET cc_start: 0.9154 (mmp) cc_final: 0.8822 (mmt) REVERT: E 120 MET cc_start: 0.9249 (mmp) cc_final: 0.8953 (mmm) REVERT: E 800 MET cc_start: 0.9156 (mpp) cc_final: 0.8840 (ptt) REVERT: E 802 MET cc_start: 0.7080 (ppp) cc_final: 0.6599 (ppp) REVERT: E 964 MET cc_start: 0.8516 (tpp) cc_final: 0.8230 (tpp) REVERT: E 1009 MET cc_start: 0.9133 (mmp) cc_final: 0.8854 (mmm) REVERT: E 1313 MET cc_start: 0.8054 (tmm) cc_final: 0.7712 (tmm) REVERT: E 1435 MET cc_start: 0.8360 (tpt) cc_final: 0.8039 (tpt) REVERT: E 1522 MET cc_start: 0.9401 (tpt) cc_final: 0.8656 (tpp) REVERT: E 1560 MET cc_start: 0.6573 (ppp) cc_final: 0.6103 (ppp) REVERT: E 1597 MET cc_start: 0.8722 (tpp) cc_final: 0.8180 (ttm) REVERT: F 45 MET cc_start: 0.8065 (tpt) cc_final: 0.7853 (tpt) outliers start: 2 outliers final: 0 residues processed: 168 average time/residue: 0.1912 time to fit residues: 54.3771 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 : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 373 optimal weight: 1.9990 chunk 397 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 385 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1035 GLN ** B1424 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** ** 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** 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 = 0.3649 r_free = 0.3649 target = 0.051607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.030164 restraints weight = 279303.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.030834 restraints weight = 182649.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.031272 restraints weight = 139949.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.031659 restraints weight = 119763.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.031867 restraints weight = 108144.436| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33556 Z= 0.158 Angle : 0.658 16.327 45324 Z= 0.335 Chirality : 0.043 0.207 5024 Planarity : 0.005 0.067 5796 Dihedral : 5.250 80.410 4394 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.05 % Allowed : 2.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.13), residues: 4022 helix: 0.41 (0.12), residues: 1998 sheet: -1.12 (0.22), residues: 500 loop : -1.24 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 683 TYR 0.019 0.002 TYR B1289 PHE 0.018 0.002 PHE E 184 TRP 0.017 0.002 TRP C 56 HIS 0.006 0.001 HIS B 533 Details of bonding type rmsd covalent geometry : bond 0.00340 (33556) covalent geometry : angle 0.65828 (45324) hydrogen bonds : bond 0.04032 ( 1685) hydrogen bonds : angle 5.44598 ( 4893) *********************** 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 170 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 LYS cc_start: 0.9299 (pptt) cc_final: 0.8855 (ttmt) REVERT: A 692 MET cc_start: 0.9116 (mmp) cc_final: 0.8802 (mmm) REVERT: B 1 MET cc_start: 0.4448 (mmp) cc_final: 0.3693 (tpp) REVERT: B 12 TYR cc_start: 0.7846 (m-80) cc_final: 0.7512 (m-80) REVERT: B 115 ARG cc_start: 0.9122 (mmm-85) cc_final: 0.8881 (mmm-85) REVERT: B 120 MET cc_start: 0.9150 (mmp) cc_final: 0.8703 (mmm) REVERT: B 306 MET cc_start: 0.3154 (mmm) cc_final: 0.1441 (ttt) REVERT: B 431 MET cc_start: 0.5388 (mmm) cc_final: 0.5088 (mmm) REVERT: B 964 MET cc_start: 0.8012 (tpt) cc_final: 0.7543 (tpt) REVERT: B 1011 MET cc_start: 0.8772 (tpp) cc_final: 0.8292 (tpp) REVERT: B 1035 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: B 1038 PHE cc_start: 0.7848 (p90) cc_final: 0.7403 (p90) REVERT: B 1243 TYR cc_start: 0.8837 (m-80) cc_final: 0.8469 (m-80) REVERT: B 1435 MET cc_start: 0.8510 (tpt) cc_final: 0.8267 (tpt) REVERT: B 1522 MET cc_start: 0.9197 (tpt) cc_final: 0.8357 (tpp) REVERT: B 1560 MET cc_start: 0.7559 (ptm) cc_final: 0.7009 (ttp) REVERT: D 692 MET cc_start: 0.9159 (mmp) cc_final: 0.8868 (mmm) REVERT: E 120 MET cc_start: 0.9258 (mmp) cc_final: 0.8854 (mmt) REVERT: E 800 MET cc_start: 0.9257 (mpp) cc_final: 0.8943 (ptt) REVERT: E 802 MET cc_start: 0.7245 (ppp) cc_final: 0.6979 (ppp) REVERT: E 964 MET cc_start: 0.8499 (tpp) cc_final: 0.8228 (tpp) REVERT: E 1009 MET cc_start: 0.9056 (mmp) cc_final: 0.8835 (mmm) REVERT: E 1313 MET cc_start: 0.8149 (tmm) cc_final: 0.7798 (tmm) REVERT: E 1435 MET cc_start: 0.8308 (tpt) cc_final: 0.7955 (tpt) REVERT: E 1522 MET cc_start: 0.9358 (tpt) cc_final: 0.8649 (tpp) REVERT: E 1560 MET cc_start: 0.6703 (ppp) cc_final: 0.6188 (ppp) REVERT: E 1597 MET cc_start: 0.8775 (tpp) cc_final: 0.8247 (ttm) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.1957 time to fit residues: 56.6602 Evaluate side-chains 139 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 285 optimal weight: 10.0000 chunk 377 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 393 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 216 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 386 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 ASN B 412 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** ** 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** ** C 39 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** ** 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** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.051156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.030129 restraints weight = 283635.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.030531 restraints weight = 191119.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.030896 restraints weight = 145036.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.031100 restraints weight = 122404.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.031404 restraints weight = 109536.076| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 33556 Z= 0.177 Angle : 0.682 17.439 45324 Z= 0.349 Chirality : 0.044 0.210 5024 Planarity : 0.005 0.125 5796 Dihedral : 5.308 80.081 4394 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.03 % Allowed : 2.08 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.13), residues: 4022 helix: 0.38 (0.12), residues: 1992 sheet: -1.17 (0.22), residues: 510 loop : -1.28 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1627 TYR 0.016 0.002 TYR E1046 PHE 0.018 0.002 PHE E 184 TRP 0.016 0.002 TRP C 56 HIS 0.005 0.001 HIS E 949 Details of bonding type rmsd covalent geometry : bond 0.00376 (33556) covalent geometry : angle 0.68206 (45324) hydrogen bonds : bond 0.04112 ( 1685) hydrogen bonds : angle 5.50617 ( 4893) *********************** 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 168 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 LYS cc_start: 0.9301 (pptt) cc_final: 0.8866 (ttmt) REVERT: A 677 MET cc_start: 0.7445 (mmp) cc_final: 0.6247 (mmp) REVERT: A 692 MET cc_start: 0.9128 (mmp) cc_final: 0.8822 (mmm) REVERT: B 1 MET cc_start: 0.5478 (mmp) cc_final: 0.4603 (tpp) REVERT: B 12 TYR cc_start: 0.7975 (m-80) cc_final: 0.7635 (m-80) REVERT: B 115 ARG cc_start: 0.9106 (mmm-85) cc_final: 0.8902 (mmm-85) REVERT: B 120 MET cc_start: 0.9139 (mmp) cc_final: 0.8652 (mmm) REVERT: B 431 MET cc_start: 0.5462 (mmm) cc_final: 0.5200 (mmm) REVERT: B 964 MET cc_start: 0.7918 (tpt) cc_final: 0.7536 (tpt) REVERT: B 1009 MET cc_start: 0.9119 (mmp) cc_final: 0.8791 (mmm) REVERT: B 1011 MET cc_start: 0.8670 (tpp) cc_final: 0.8423 (tpp) REVERT: B 1038 PHE cc_start: 0.7765 (p90) cc_final: 0.7311 (p90) REVERT: B 1243 TYR cc_start: 0.8912 (m-80) cc_final: 0.8557 (m-80) REVERT: B 1435 MET cc_start: 0.8522 (tpt) cc_final: 0.8283 (tpt) REVERT: B 1522 MET cc_start: 0.9239 (tpt) cc_final: 0.8408 (tpp) REVERT: B 1560 MET cc_start: 0.7638 (ptm) cc_final: 0.7045 (ttp) REVERT: D 692 MET cc_start: 0.9134 (mmp) cc_final: 0.8840 (mmm) REVERT: E 120 MET cc_start: 0.9259 (mmp) cc_final: 0.8862 (mmt) REVERT: E 800 MET cc_start: 0.9279 (mpp) cc_final: 0.8944 (ptt) REVERT: E 802 MET cc_start: 0.7239 (ppp) cc_final: 0.6996 (ppp) REVERT: E 964 MET cc_start: 0.8500 (tpp) cc_final: 0.8048 (tpp) REVERT: E 1009 MET cc_start: 0.9149 (mmp) cc_final: 0.8866 (mmm) REVERT: E 1038 PHE cc_start: 0.7823 (p90) cc_final: 0.7575 (p90) REVERT: E 1435 MET cc_start: 0.8367 (tpt) cc_final: 0.7997 (tpt) REVERT: E 1522 MET cc_start: 0.9384 (tpt) cc_final: 0.8688 (tpp) REVERT: E 1560 MET cc_start: 0.6556 (ppp) cc_final: 0.6191 (ppp) REVERT: E 1597 MET cc_start: 0.8814 (tpp) cc_final: 0.8508 (ttm) REVERT: F 45 MET cc_start: 0.8514 (tpt) cc_final: 0.8313 (tpt) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.1878 time to fit residues: 53.6026 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 : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 120 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 393 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 364 optimal weight: 0.9980 chunk 302 optimal weight: 10.0000 chunk 363 optimal weight: 2.9990 chunk 288 optimal weight: 20.0000 chunk 154 optimal weight: 0.8980 chunk 312 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 ASN ** 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** ** 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** ** E 130 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 944 ASN E1359 GLN ** E1424 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.052512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.031499 restraints weight = 310306.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.032281 restraints weight = 200079.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.032206 restraints weight = 144843.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.032345 restraints weight = 119037.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.032345 restraints weight = 107315.339| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3340 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= 0.133 Angle : 0.675 18.841 45324 Z= 0.338 Chirality : 0.044 0.204 5024 Planarity : 0.005 0.080 5796 Dihedral : 5.186 80.946 4394 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.03 % Allowed : 1.15 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.14), residues: 4022 helix: 0.50 (0.12), residues: 1996 sheet: -0.99 (0.23), residues: 500 loop : -1.25 (0.17), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1627 TYR 0.023 0.001 TYR B 572 PHE 0.022 0.001 PHE E 184 TRP 0.018 0.002 TRP E 102 HIS 0.006 0.001 HIS E 187 Details of bonding type rmsd covalent geometry : bond 0.00292 (33556) covalent geometry : angle 0.67518 (45324) hydrogen bonds : bond 0.03919 ( 1685) hydrogen bonds : angle 5.37263 ( 4893) *********************** 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 180 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 LYS cc_start: 0.9288 (pptt) cc_final: 0.8852 (ttmt) REVERT: A 677 MET cc_start: 0.7578 (mmp) cc_final: 0.6594 (mmp) REVERT: A 692 MET cc_start: 0.9068 (mmp) cc_final: 0.8714 (mmm) REVERT: B 1 MET cc_start: 0.6002 (mmp) cc_final: 0.5317 (tpp) REVERT: B 12 TYR cc_start: 0.7792 (m-80) cc_final: 0.7405 (m-80) REVERT: B 115 ARG cc_start: 0.9062 (mmm-85) cc_final: 0.8848 (mmm-85) REVERT: B 120 MET cc_start: 0.9133 (mmp) cc_final: 0.8616 (mmm) REVERT: B 306 MET cc_start: 0.2471 (mmm) cc_final: 0.1108 (ttt) REVERT: B 964 MET cc_start: 0.8387 (tpt) cc_final: 0.7971 (tpt) REVERT: B 1009 MET cc_start: 0.9025 (mmp) cc_final: 0.8663 (mmm) REVERT: B 1011 MET cc_start: 0.8624 (tpp) cc_final: 0.8374 (tpp) REVERT: B 1038 PHE cc_start: 0.7774 (p90) cc_final: 0.7397 (p90) REVERT: B 1146 MET cc_start: 0.8255 (pmm) cc_final: 0.7519 (pmm) REVERT: B 1243 TYR cc_start: 0.8998 (m-80) cc_final: 0.8463 (m-80) REVERT: B 1435 MET cc_start: 0.8508 (tpt) cc_final: 0.8275 (tpt) REVERT: B 1482 MET cc_start: 0.7456 (mmm) cc_final: 0.7254 (mmm) REVERT: B 1522 MET cc_start: 0.9196 (tpt) cc_final: 0.8456 (tpp) REVERT: B 1560 MET cc_start: 0.7410 (ptm) cc_final: 0.7008 (ttp) REVERT: D 692 MET cc_start: 0.9077 (mmp) cc_final: 0.8768 (mmm) REVERT: E 120 MET cc_start: 0.9266 (mmp) cc_final: 0.8857 (mmt) REVERT: E 800 MET cc_start: 0.9287 (mpp) cc_final: 0.8997 (ptt) REVERT: E 987 MET cc_start: 0.8161 (mmm) cc_final: 0.7838 (mmp) REVERT: E 1009 MET cc_start: 0.9107 (mmp) cc_final: 0.8876 (mmm) REVERT: E 1038 PHE cc_start: 0.7926 (p90) cc_final: 0.7692 (p90) REVERT: E 1522 MET cc_start: 0.9354 (tpt) cc_final: 0.8625 (tpp) REVERT: E 1549 MET cc_start: 0.8748 (mmp) cc_final: 0.8469 (mmm) REVERT: E 1560 MET cc_start: 0.6523 (ppp) cc_final: 0.6028 (ppp) REVERT: E 1597 MET cc_start: 0.8804 (tpp) cc_final: 0.8274 (ttm) REVERT: F 45 MET cc_start: 0.8466 (tpt) cc_final: 0.8251 (tpt) REVERT: F 91 GLU cc_start: 0.9193 (mp0) cc_final: 0.8970 (mp0) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1886 time to fit residues: 57.9073 Evaluate side-chains 144 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 272 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 166 optimal weight: 0.3980 chunk 385 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 389 optimal weight: 0.8980 chunk 364 optimal weight: 0.7980 chunk 216 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 124 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 554 ASN A 596 GLN ** 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** B 944 ASN ** B1424 GLN ** 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** D 660 HIS E 556 ASN ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 944 ASN ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 GLN F 39 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.052773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.032539 restraints weight = 304688.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.032391 restraints weight = 209910.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.032918 restraints weight = 159800.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.033019 restraints weight = 130041.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.033312 restraints weight = 121279.790| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 33556 Z= 0.126 Angle : 0.674 18.308 45324 Z= 0.338 Chirality : 0.044 0.219 5024 Planarity : 0.004 0.071 5796 Dihedral : 5.098 81.159 4394 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.14), residues: 4022 helix: 0.58 (0.12), residues: 1996 sheet: -0.89 (0.23), residues: 500 loop : -1.27 (0.17), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1627 TYR 0.037 0.001 TYR E1328 PHE 0.025 0.001 PHE E 764 TRP 0.018 0.001 TRP E 102 HIS 0.004 0.001 HIS E 949 Details of bonding type rmsd covalent geometry : bond 0.00276 (33556) covalent geometry : angle 0.67424 (45324) hydrogen bonds : bond 0.03812 ( 1685) hydrogen bonds : angle 5.33131 ( 4893) ********************** 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 185 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 182 time to evaluate : 1.154 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: 0.9316 (pptt) cc_final: 0.8972 (ttmt) REVERT: A 677 MET cc_start: 0.7391 (mmp) cc_final: 0.6397 (mmp) REVERT: A 692 MET cc_start: 0.9097 (mmp) cc_final: 0.8729 (mmm) REVERT: B 1 MET cc_start: 0.5885 (mmp) cc_final: 0.5262 (tpp) REVERT: B 12 TYR cc_start: 0.7913 (m-80) cc_final: 0.7565 (m-80) REVERT: B 115 ARG cc_start: 0.9076 (mmm-85) cc_final: 0.8853 (mmm-85) REVERT: B 120 MET cc_start: 0.9136 (mmp) cc_final: 0.8643 (mmm) REVERT: B 306 MET cc_start: 0.2443 (mmm) cc_final: 0.1391 (ttt) REVERT: B 659 GLU cc_start: 0.7882 (mp0) cc_final: 0.7621 (mp0) REVERT: B 681 MET cc_start: 0.6260 (ptp) cc_final: 0.5725 (ppp) REVERT: B 961 LEU cc_start: 0.9598 (mt) cc_final: 0.9392 (mp) REVERT: B 964 MET cc_start: 0.8358 (tpt) cc_final: 0.7912 (tpt) REVERT: B 992 MET cc_start: 0.9019 (ttp) cc_final: 0.8421 (ppp) REVERT: B 1009 MET cc_start: 0.9122 (mmp) cc_final: 0.8675 (mmm) REVERT: B 1038 PHE cc_start: 0.7607 (p90) cc_final: 0.7215 (p90) REVERT: B 1146 MET cc_start: 0.8509 (pmm) cc_final: 0.7747 (pmm) REVERT: B 1243 TYR cc_start: 0.9159 (m-80) cc_final: 0.8665 (m-80) REVERT: B 1435 MET cc_start: 0.8737 (tpt) cc_final: 0.8355 (tpt) REVERT: B 1522 MET cc_start: 0.9313 (tpt) cc_final: 0.8593 (tpp) REVERT: B 1560 MET cc_start: 0.7423 (ptm) cc_final: 0.6987 (ttp) REVERT: C 31 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7975 (mm-30) REVERT: D 569 ARG cc_start: 0.3434 (mmt180) cc_final: 0.3140 (ptp90) REVERT: D 692 MET cc_start: 0.9135 (mmp) cc_final: 0.8731 (mmt) REVERT: E 306 MET cc_start: 0.2644 (mmm) cc_final: 0.2173 (mmm) REVERT: E 800 MET cc_start: 0.9151 (mpp) cc_final: 0.8881 (ptt) REVERT: E 987 MET cc_start: 0.8193 (mmm) cc_final: 0.7848 (mmp) REVERT: E 1009 MET cc_start: 0.9200 (mmp) cc_final: 0.8903 (mmm) REVERT: E 1038 PHE cc_start: 0.7805 (p90) cc_final: 0.7530 (p90) REVERT: E 1313 MET cc_start: 0.7078 (tmm) cc_final: 0.6781 (tmm) REVERT: E 1522 MET cc_start: 0.9442 (tpt) cc_final: 0.8729 (tpp) REVERT: E 1560 MET cc_start: 0.6483 (ppp) cc_final: 0.6032 (ppp) REVERT: E 1597 MET cc_start: 0.8763 (tpp) cc_final: 0.8550 (tpt) REVERT: F 91 GLU cc_start: 0.9117 (mp0) cc_final: 0.8885 (mp0) outliers start: 3 outliers final: 0 residues processed: 184 average time/residue: 0.1851 time to fit residues: 57.4016 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 : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 350 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 293 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 326 optimal weight: 0.8980 chunk 358 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 377 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 185 optimal weight: 0.0370 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 596 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 ASN ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** 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 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.052111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.032086 restraints weight = 276132.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.032243 restraints weight = 193317.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.032573 restraints weight = 151952.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.032959 restraints weight = 133631.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.033151 restraints weight = 121382.484| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3639 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= 0.129 Angle : 0.665 19.785 45324 Z= 0.334 Chirality : 0.044 0.239 5024 Planarity : 0.004 0.065 5796 Dihedral : 5.053 80.393 4394 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.08 % Allowed : 0.52 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.14), residues: 4022 helix: 0.66 (0.12), residues: 1988 sheet: -0.83 (0.23), residues: 500 loop : -1.26 (0.17), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1627 TYR 0.049 0.001 TYR B1231 PHE 0.019 0.001 PHE E 764 TRP 0.017 0.001 TRP E 102 HIS 0.005 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00283 (33556) covalent geometry : angle 0.66542 (45324) hydrogen bonds : bond 0.03785 ( 1685) hydrogen bonds : angle 5.30791 ( 4893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7276.81 seconds wall clock time: 126 minutes 5.78 seconds (7565.78 seconds total)