Starting phenix.real_space_refine on Fri Mar 6 17:24:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dpa_30802/03_2026/7dpa_30802.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dpa_30802/03_2026/7dpa_30802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dpa_30802/03_2026/7dpa_30802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dpa_30802/03_2026/7dpa_30802.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dpa_30802/03_2026/7dpa_30802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dpa_30802/03_2026/7dpa_30802.map" } resolution = 3.8 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= 0.001 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 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/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: 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: "B" 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: "C" 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: "D" 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: "E" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1385 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain: "F" Number of atoms: 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} Time building chain proxies: 7.17, per 1000 atoms: 0.22 Number of scatterers: 32858 At special positions: 0 Unit cell: (243.19, 163.51, 155.21, 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: 2.28 Conformation dependent library (CDL) restraints added in 1.3 seconds 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7696 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 24 sheets defined 51.9% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 84 through 105 removed outlier: 3.768A pdb=" N VAL A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 133 removed outlier: 4.345A pdb=" N SER A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 180 through 208 Processing helix chain 'A' and resid 296 through 300 removed outlier: 4.105A pdb=" N ILE A 300 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 removed outlier: 3.780A pdb=" N VAL A 337 " --> pdb=" O ILE A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.820A pdb=" N ARG A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 387 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 404 through 412 removed outlier: 3.563A pdb=" N GLY A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 429 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 518 through 524 Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.739A pdb=" N MET A 595 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 596 " --> pdb=" O LYS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 641 removed outlier: 3.673A pdb=" N GLY A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 676 Processing helix chain 'A' and resid 678 through 704 removed outlier: 4.267A pdb=" N GLU A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 698 " --> pdb=" O PHE A 694 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 745 through 751 Processing helix chain 'A' and resid 756 through 769 removed outlier: 4.148A pdb=" N PHE A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 778 through 781 Processing helix chain 'A' and resid 785 through 804 removed outlier: 3.626A pdb=" N ASN A 789 " --> pdb=" O ASP A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 818 removed outlier: 3.950A pdb=" N LYS A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 826 removed outlier: 4.446A pdb=" N ILE A 823 " --> pdb=" O TYR A 819 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 846 removed outlier: 4.203A pdb=" N SER A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 866 removed outlier: 3.771A pdb=" N ASN A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 891 removed outlier: 3.900A pdb=" N CYS A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU A 876 " --> pdb=" O SER A 872 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) Proline residue: A 880 - end of helix removed outlier: 4.049A pdb=" N ASP A 891 " --> pdb=" O SER A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 915 removed outlier: 4.578A pdb=" N ASP A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU A 900 " --> pdb=" O LYS A 896 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 943 removed outlier: 6.323A pdb=" N ARG A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG A 935 " --> pdb=" O ARG A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 964 removed outlier: 3.707A pdb=" N PHE A 953 " --> pdb=" O HIS A 949 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 970 Processing helix chain 'A' and resid 979 through 998 removed outlier: 3.998A pdb=" N PHE A 985 " --> pdb=" O ASP A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1032 removed outlier: 3.507A pdb=" N LEU A1028 " --> pdb=" O PHE A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1055 removed outlier: 4.208A pdb=" N ASN A1045 " --> pdb=" O GLN A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1064 Processing helix chain 'A' and resid 1067 through 1075 Processing helix chain 'A' and resid 1078 through 1094 removed outlier: 3.526A pdb=" N GLU A1082 " --> pdb=" O ASP A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1099 removed outlier: 4.245A pdb=" N ILE A1099 " --> pdb=" O PRO A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1114 removed outlier: 3.657A pdb=" N ILE A1109 " --> pdb=" O MET A1105 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU A1111 " --> pdb=" O GLY A1107 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A1112 " --> pdb=" O PRO A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1125 Processing helix chain 'A' and resid 1126 through 1137 Processing helix chain 'A' and resid 1138 through 1142 removed outlier: 3.653A pdb=" N GLY A1142 " --> pdb=" O SER A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1162 removed outlier: 3.860A pdb=" N GLU A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1180 Processing helix chain 'A' and resid 1184 through 1215 removed outlier: 3.567A pdb=" N SER A1188 " --> pdb=" O LYS A1184 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET A1212 " --> pdb=" O ARG A1208 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A1215 " --> pdb=" O ILE A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1235 Processing helix chain 'A' and resid 1236 through 1255 Processing helix chain 'A' and resid 1256 through 1269 Processing helix chain 'A' and resid 1279 through 1283 removed outlier: 3.947A pdb=" N LEU A1282 " --> pdb=" O VAL A1279 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A1283 " --> pdb=" O PRO A1280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1279 through 1283' Processing helix chain 'A' and resid 1292 through 1311 Processing helix chain 'A' and resid 1313 through 1332 removed outlier: 3.728A pdb=" N ALA A1317 " --> pdb=" O MET A1313 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU A1323 " --> pdb=" O LYS A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1355 removed outlier: 3.565A pdb=" N ALA A1355 " --> pdb=" O ASN A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1401 Processing helix chain 'A' and resid 1447 through 1455 removed outlier: 3.928A pdb=" N LEU A1451 " --> pdb=" O PRO A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1538 Processing helix chain 'A' and resid 1544 through 1556 Processing helix chain 'A' and resid 1561 through 1570 Processing helix chain 'A' and resid 1572 through 1579 removed outlier: 3.741A pdb=" N LEU A1576 " --> pdb=" O THR A1572 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1611 Proline residue: A1598 - end of helix Processing helix chain 'A' and resid 1615 through 1635 Processing helix chain 'B' and resid 15 through 25 removed outlier: 3.859A pdb=" N LEU B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.591A pdb=" N ARG B 66 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 96 Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'C' and resid 531 through 540 Processing helix chain 'C' and resid 541 through 559 removed outlier: 3.768A pdb=" N LEU C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C 546 " --> pdb=" O PRO C 542 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 559 " --> pdb=" O ARG C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 640 Processing helix chain 'C' and resid 658 through 672 removed outlier: 3.554A pdb=" N TYR C 662 " --> pdb=" O ASP C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 696 Processing helix chain 'D' and resid 84 through 105 removed outlier: 3.769A pdb=" N VAL D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 133 removed outlier: 4.345A pdb=" N SER D 133 " --> pdb=" O SER D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 180 through 208 Processing helix chain 'D' and resid 296 through 300 removed outlier: 4.105A pdb=" N ILE D 300 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 removed outlier: 3.780A pdb=" N VAL D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 364 removed outlier: 3.820A pdb=" N ARG D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 387 Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 404 through 412 removed outlier: 3.563A pdb=" N GLY D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 429 Processing helix chain 'D' and resid 491 through 495 Processing helix chain 'D' and resid 518 through 524 Processing helix chain 'D' and resid 575 through 579 Processing helix chain 'D' and resid 582 through 587 Processing helix chain 'D' and resid 591 through 597 removed outlier: 3.738A pdb=" N MET D 595 " --> pdb=" O THR D 591 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU D 596 " --> pdb=" O LYS D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 removed outlier: 3.673A pdb=" N GLY D 639 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 676 Processing helix chain 'D' and resid 678 through 704 removed outlier: 4.266A pdb=" N GLU D 682 " --> pdb=" O ASN D 678 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL D 698 " --> pdb=" O PHE D 694 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 714 through 721 Processing helix chain 'D' and resid 727 through 740 Processing helix chain 'D' and resid 745 through 751 Processing helix chain 'D' and resid 756 through 769 removed outlier: 4.148A pdb=" N PHE D 764 " --> pdb=" O LEU D 760 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE D 767 " --> pdb=" O LEU D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 777 Processing helix chain 'D' and resid 778 through 781 Processing helix chain 'D' and resid 785 through 804 removed outlier: 3.626A pdb=" N ASN D 789 " --> pdb=" O ASP D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 818 removed outlier: 3.950A pdb=" N LYS D 818 " --> pdb=" O GLY D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 826 removed outlier: 4.447A pdb=" N ILE D 823 " --> pdb=" O TYR D 819 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 824 " --> pdb=" O LEU D 820 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP D 826 " --> pdb=" O SER D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 846 removed outlier: 4.203A pdb=" N SER D 846 " --> pdb=" O LYS D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 866 removed outlier: 3.772A pdb=" N ASN D 858 " --> pdb=" O ARG D 854 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER D 866 " --> pdb=" O LYS D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 891 removed outlier: 3.901A pdb=" N CYS D 874 " --> pdb=" O ARG D 870 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLU D 876 " --> pdb=" O SER D 872 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 877 " --> pdb=" O GLU D 873 " (cutoff:3.500A) Proline residue: D 880 - end of helix removed outlier: 4.049A pdb=" N ASP D 891 " --> pdb=" O SER D 887 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 915 removed outlier: 4.577A pdb=" N ASP D 898 " --> pdb=" O SER D 894 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU D 900 " --> pdb=" O LYS D 896 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA D 901 " --> pdb=" O PRO D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 943 removed outlier: 6.323A pdb=" N ARG D 934 " --> pdb=" O GLU D 930 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ARG D 935 " --> pdb=" O ARG D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 949 through 964 removed outlier: 3.707A pdb=" N PHE D 953 " --> pdb=" O HIS D 949 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET D 964 " --> pdb=" O LEU D 960 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 970 Processing helix chain 'D' and resid 979 through 998 removed outlier: 3.997A pdb=" N PHE D 985 " --> pdb=" O ASP D 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1032 removed outlier: 3.507A pdb=" N LEU D1028 " --> pdb=" O PHE D1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1055 removed outlier: 4.208A pdb=" N ASN D1045 " --> pdb=" O GLN D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1064 Processing helix chain 'D' and resid 1067 through 1075 Processing helix chain 'D' and resid 1078 through 1094 removed outlier: 3.525A pdb=" N GLU D1082 " --> pdb=" O ASP D1078 " (cutoff:3.500A) Processing helix chain 'D' and resid 1095 through 1099 removed outlier: 4.246A pdb=" N ILE D1099 " --> pdb=" O PRO D1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 1105 through 1114 removed outlier: 3.657A pdb=" N ILE D1109 " --> pdb=" O MET D1105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D1110 " --> pdb=" O VAL D1106 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU D1111 " --> pdb=" O GLY D1107 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D1112 " --> pdb=" O PRO D1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1125 Processing helix chain 'D' and resid 1126 through 1137 Processing helix chain 'D' and resid 1138 through 1142 removed outlier: 3.653A pdb=" N GLY D1142 " --> pdb=" O SER D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1162 removed outlier: 3.860A pdb=" N GLU D1150 " --> pdb=" O MET D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1165 through 1180 Processing helix chain 'D' and resid 1184 through 1215 removed outlier: 3.567A pdb=" N SER D1188 " --> pdb=" O LYS D1184 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET D1212 " --> pdb=" O ARG D1208 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU D1215 " --> pdb=" O ILE D1211 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1235 Processing helix chain 'D' and resid 1236 through 1255 Processing helix chain 'D' and resid 1256 through 1269 Processing helix chain 'D' and resid 1279 through 1283 removed outlier: 3.946A pdb=" N LEU D1282 " --> pdb=" O VAL D1279 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D1283 " --> pdb=" O PRO D1280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1279 through 1283' Processing helix chain 'D' and resid 1292 through 1311 Processing helix chain 'D' and resid 1313 through 1332 removed outlier: 3.729A pdb=" N ALA D1317 " --> pdb=" O MET D1313 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU D1323 " --> pdb=" O LYS D1319 " (cutoff:3.500A) Processing helix chain 'D' and resid 1334 through 1355 removed outlier: 3.565A pdb=" N ALA D1355 " --> pdb=" O ASN D1351 " (cutoff:3.500A) Processing helix chain 'D' and resid 1390 through 1401 Processing helix chain 'D' and resid 1447 through 1455 removed outlier: 3.927A pdb=" N LEU D1451 " --> pdb=" O PRO D1447 " (cutoff:3.500A) Processing helix chain 'D' and resid 1513 through 1538 Processing helix chain 'D' and resid 1544 through 1556 Processing helix chain 'D' and resid 1561 through 1570 Processing helix chain 'D' and resid 1572 through 1579 removed outlier: 3.741A pdb=" N LEU D1576 " --> pdb=" O THR D1572 " (cutoff:3.500A) Processing helix chain 'D' and resid 1584 through 1611 Proline residue: D1598 - end of helix Processing helix chain 'D' and resid 1615 through 1635 Processing helix chain 'E' and resid 15 through 25 removed outlier: 3.859A pdb=" N LEU E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR E 25 " --> pdb=" O ILE E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.591A pdb=" N ARG E 66 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 96 Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'F' and resid 531 through 540 Processing helix chain 'F' and resid 541 through 559 removed outlier: 3.768A pdb=" N LEU F 545 " --> pdb=" O GLN F 541 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU F 546 " --> pdb=" O PRO F 542 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY F 559 " --> pdb=" O ARG F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 640 Processing helix chain 'F' and resid 658 through 672 removed outlier: 3.554A pdb=" N TYR F 662 " --> pdb=" O ASP F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 696 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 234 removed outlier: 7.424A pdb=" N PHE A 228 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 245 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 234 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 239 " --> pdb=" O ASN A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 removed outlier: 3.588A pdb=" N GLU A 307 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS A 305 " --> pdb=" O TRP A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 469 through 474 removed outlier: 3.776A pdb=" N SER A 471 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 548 through 549 removed outlier: 3.600A pdb=" N VAL A 549 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR A 572 " --> pdb=" O VAL A 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1362 through 1363 removed outlier: 4.371A pdb=" N TYR A1362 " --> pdb=" O VAL A1431 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLN A1460 " --> pdb=" O THR A1491 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1365 through 1366 Processing sheet with id=AA8, first strand: chain 'A' and resid 1467 through 1469 Processing sheet with id=AA9, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.520A pdb=" N VAL B 8 " --> pdb=" O TRP B 56 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N VAL B 7 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N CYS B 81 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL B 9 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N SER B 83 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE B 78 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL B 113 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE B 80 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N THR B 115 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE B 82 " --> pdb=" O THR B 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 576 through 579 removed outlier: 4.646A pdb=" N TYR C 576 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY C 589 " --> pdb=" O TYR C 576 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 616 through 618 removed outlier: 4.676A pdb=" N PHE C 642 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 654 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 652 " --> pdb=" O ILE C 644 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR C 646 " --> pdb=" O CYS C 650 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS C 650 " --> pdb=" O TYR C 646 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB5, first strand: chain 'D' and resid 228 through 234 removed outlier: 7.425A pdb=" N PHE D 228 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 245 " --> pdb=" O PHE D 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN D 234 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA D 239 " --> pdb=" O ASN D 234 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 269 through 272 removed outlier: 3.587A pdb=" N GLU D 307 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS D 305 " --> pdb=" O TRP D 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 469 through 474 removed outlier: 3.777A pdb=" N SER D 471 " --> pdb=" O ARG D 528 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 548 through 549 removed outlier: 3.600A pdb=" N VAL D 549 " --> pdb=" O TYR D 572 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR D 572 " --> pdb=" O VAL D 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 1362 through 1363 removed outlier: 4.371A pdb=" N TYR D1362 " --> pdb=" O VAL D1431 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLN D1460 " --> pdb=" O THR D1491 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 1365 through 1366 Processing sheet with id=AC2, first strand: chain 'D' and resid 1467 through 1469 Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AC4, first strand: chain 'E' and resid 56 through 57 removed outlier: 3.520A pdb=" N VAL E 8 " --> pdb=" O TRP E 56 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N VAL E 7 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N CYS E 81 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL E 9 " --> pdb=" O CYS E 81 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N SER E 83 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE E 78 " --> pdb=" O ILE E 111 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL E 113 " --> pdb=" O PHE E 78 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE E 80 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N THR E 115 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE E 82 " --> pdb=" O THR E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 576 through 579 removed outlier: 4.646A pdb=" N TYR F 576 " --> pdb=" O GLY F 589 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY F 589 " --> pdb=" O TYR F 576 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 616 through 618 removed outlier: 4.676A pdb=" N PHE F 642 " --> pdb=" O PHE F 654 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE F 654 " --> pdb=" O PHE F 642 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU F 652 " --> pdb=" O ILE F 644 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR F 646 " --> pdb=" O CYS F 650 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS F 650 " --> pdb=" O TYR F 646 " (cutoff:3.500A) 1444 hydrogen bonds defined for protein. 4230 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: 6.20 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9652 1.33 - 1.45: 5087 1.45 - 1.57: 18521 1.57 - 1.69: 2 1.69 - 1.81: 294 Bond restraints: 33556 Sorted by residual: bond pdb=" CB TYR D1301 " pdb=" CG TYR D1301 " ideal model delta sigma weight residual 1.512 1.470 0.042 2.20e-02 2.07e+03 3.63e+00 bond pdb=" CB TYR A1301 " pdb=" CG TYR A1301 " ideal model delta sigma weight residual 1.512 1.471 0.041 2.20e-02 2.07e+03 3.53e+00 bond pdb=" CB PHE A1308 " pdb=" CG PHE A1308 " ideal model delta sigma weight residual 1.502 1.459 0.043 2.30e-02 1.89e+03 3.43e+00 bond pdb=" CG1 ILE A1125 " pdb=" CD1 ILE A1125 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.39e+00 bond pdb=" CB PHE D1308 " pdb=" CG PHE D1308 " ideal model delta sigma weight residual 1.502 1.460 0.042 2.30e-02 1.89e+03 3.37e+00 ... (remaining 33551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 44607 2.78 - 5.56: 639 5.56 - 8.35: 62 8.35 - 11.13: 12 11.13 - 13.91: 4 Bond angle restraints: 45324 Sorted by residual: angle pdb=" CG1 ILE D 101 " pdb=" CB ILE D 101 " pdb=" CG2 ILE D 101 " ideal model delta sigma weight residual 110.70 96.79 13.91 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CG1 ILE A 101 " pdb=" CB ILE A 101 " pdb=" CG2 ILE A 101 " ideal model delta sigma weight residual 110.70 96.82 13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" CA PRO D1514 " pdb=" N PRO D1514 " pdb=" CD PRO D1514 " ideal model delta sigma weight residual 112.00 106.10 5.90 1.40e+00 5.10e-01 1.78e+01 angle pdb=" CA PRO A1514 " pdb=" N PRO A1514 " pdb=" CD PRO A1514 " ideal model delta sigma weight residual 112.00 106.16 5.84 1.40e+00 5.10e-01 1.74e+01 angle pdb=" C ARG D 157 " pdb=" N MET D 158 " pdb=" CA MET D 158 " ideal model delta sigma weight residual 121.18 113.42 7.76 1.98e+00 2.55e-01 1.54e+01 ... (remaining 45319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 18000 17.74 - 35.48: 2022 35.48 - 53.21: 362 53.21 - 70.95: 52 70.95 - 88.69: 40 Dihedral angle restraints: 20476 sinusoidal: 8586 harmonic: 11890 Sorted by residual: dihedral pdb=" CA LEU D 820 " pdb=" C LEU D 820 " pdb=" N PRO D 821 " pdb=" CA PRO D 821 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA LEU A 820 " pdb=" C LEU A 820 " pdb=" N PRO A 821 " pdb=" CA PRO A 821 " ideal model delta harmonic sigma weight residual 180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLN F 541 " pdb=" C GLN F 541 " pdb=" N PRO F 542 " pdb=" CA PRO F 542 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 20473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3846 0.057 - 0.115: 1028 0.115 - 0.172: 126 0.172 - 0.230: 20 0.230 - 0.287: 4 Chirality restraints: 5024 Sorted by residual: chirality pdb=" CG LEU A1342 " pdb=" CB LEU A1342 " pdb=" CD1 LEU A1342 " pdb=" CD2 LEU A1342 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CG LEU D1342 " pdb=" CB LEU D1342 " pdb=" CD1 LEU D1342 " pdb=" CD2 LEU D1342 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA TYR D1291 " pdb=" N TYR D1291 " pdb=" C TYR D1291 " pdb=" CB TYR D1291 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 5021 not shown) Planarity restraints: 5796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 665 " -0.026 2.00e-02 2.50e+03 2.70e-02 1.82e+01 pdb=" CG TRP C 665 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP C 665 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C 665 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 665 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 665 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 665 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 665 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 665 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 665 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 665 " 0.025 2.00e-02 2.50e+03 2.69e-02 1.81e+01 pdb=" CG TRP F 665 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP F 665 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP F 665 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 665 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 665 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 665 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 665 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 665 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 665 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D1513 " 0.068 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO D1514 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO D1514 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D1514 " 0.055 5.00e-02 4.00e+02 ... (remaining 5793 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 411 2.61 - 3.18: 31081 3.18 - 3.76: 51128 3.76 - 4.33: 69157 4.33 - 4.90: 108564 Nonbonded interactions: 260341 Sorted by model distance: nonbonded pdb=" OG1 THR A 180 " pdb=" OE1 GLN A 962 " model vdw 2.038 3.040 nonbonded pdb=" OG1 THR D 180 " pdb=" OE1 GLN D 962 " model vdw 2.038 3.040 nonbonded pdb=" O ASP D1275 " pdb=" OG1 THR D1292 " model vdw 2.064 3.040 nonbonded pdb=" O ASP A1275 " pdb=" OG1 THR A1292 " model vdw 2.065 3.040 nonbonded pdb=" O LEU D1059 " pdb=" OG1 THR D1063 " model vdw 2.067 3.040 ... (remaining 260336 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: 0.05 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: 12.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 28.300 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4101 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 33556 Z= 0.251 Angle : 0.845 13.910 45324 Z= 0.459 Chirality : 0.051 0.287 5024 Planarity : 0.006 0.100 5796 Dihedral : 15.299 88.688 12780 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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 are not related in a simple way. whole: -3.05 (0.12), residues: 4022 helix: -1.34 (0.11), residues: 1816 sheet: -2.35 (0.30), residues: 262 loop : -2.65 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 683 TYR 0.045 0.002 TYR A1262 PHE 0.053 0.002 PHE A1308 TRP 0.073 0.004 TRP C 665 HIS 0.014 0.002 HIS D 924 Details of bonding type rmsd covalent geometry : bond 0.00566 (33556) covalent geometry : angle 0.84494 (45324) hydrogen bonds : bond 0.14440 ( 1444) hydrogen bonds : angle 7.52452 ( 4230) *********************** 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 369 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 120 MET cc_start: 0.6732 (mmt) cc_final: 0.5802 (mmt) REVERT: A 353 MET cc_start: 0.0915 (mmt) cc_final: 0.0590 (mmp) REVERT: A 364 MET cc_start: 0.1966 (mtt) cc_final: 0.1691 (pmm) REVERT: A 595 MET cc_start: -0.2710 (mtt) cc_final: -0.3137 (mmt) REVERT: D 120 MET cc_start: 0.6504 (mmt) cc_final: 0.6042 (mmt) REVERT: D 306 MET cc_start: -0.1039 (pmm) cc_final: -0.2848 (ptm) REVERT: D 353 MET cc_start: 0.0562 (mmt) cc_final: 0.0341 (mmp) REVERT: D 364 MET cc_start: 0.1593 (mtt) cc_final: 0.1173 (pmm) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.2077 time to fit residues: 122.6371 Evaluate side-chains 212 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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: 0.0970 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN A1219 ASN A1401 GLN A1545 HIS ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN D 278 GLN D 394 HIS ** D 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 946 GLN D1219 ASN D1272 GLN D1401 GLN D1545 HIS ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.076566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.052399 restraints weight = 231712.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.053004 restraints weight = 172610.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.052339 restraints weight = 131216.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.052549 restraints weight = 113824.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.052767 restraints weight = 103304.702| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33556 Z= 0.181 Angle : 0.764 11.861 45324 Z= 0.398 Chirality : 0.047 0.265 5024 Planarity : 0.005 0.071 5796 Dihedral : 6.177 35.177 4394 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.93 % Allowed : 11.00 % Favored : 88.07 % 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 are not related in a simple way. whole: -2.65 (0.12), residues: 4022 helix: -0.94 (0.11), residues: 1896 sheet: -2.31 (0.29), residues: 278 loop : -2.54 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 103 TYR 0.022 0.002 TYR D 258 PHE 0.024 0.002 PHE D 795 TRP 0.026 0.002 TRP A 102 HIS 0.010 0.001 HIS D 924 Details of bonding type rmsd covalent geometry : bond 0.00388 (33556) covalent geometry : angle 0.76440 (45324) hydrogen bonds : bond 0.05481 ( 1444) hydrogen bonds : angle 6.20649 ( 4230) *********************** 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 263 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7564 (tpp) cc_final: 0.7271 (tpp) REVERT: A 364 MET cc_start: 0.3838 (mtt) cc_final: 0.3481 (pmm) REVERT: A 431 MET cc_start: 0.8546 (tpt) cc_final: 0.7965 (mmt) REVERT: A 658 MET cc_start: 0.6580 (tpp) cc_final: 0.6247 (tpp) REVERT: A 957 MET cc_start: 0.9483 (ttp) cc_final: 0.8997 (ptm) REVERT: A 1102 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8728 (mt) REVERT: A 1221 MET cc_start: 0.8611 (mtt) cc_final: 0.8377 (mmt) REVERT: A 1522 MET cc_start: 0.9118 (mmm) cc_final: 0.8728 (tpp) REVERT: A 1549 MET cc_start: 0.7637 (mmm) cc_final: 0.6772 (mmm) REVERT: B 45 MET cc_start: 0.8141 (ptm) cc_final: 0.7174 (tmm) REVERT: C 720 TYR cc_start: 0.1885 (OUTLIER) cc_final: 0.1240 (t80) REVERT: D 243 MET cc_start: -0.2864 (mmt) cc_final: -0.3337 (mmt) REVERT: D 306 MET cc_start: -0.4861 (pmm) cc_final: -0.5586 (ptm) REVERT: D 364 MET cc_start: 0.3584 (mtt) cc_final: 0.3226 (pmm) REVERT: D 431 MET cc_start: 0.8562 (tpt) cc_final: 0.8321 (mmt) REVERT: D 658 MET cc_start: 0.6538 (tpp) cc_final: 0.6303 (tpp) REVERT: D 681 MET cc_start: 0.5263 (tmm) cc_final: 0.4388 (mmt) REVERT: D 683 MET cc_start: 0.7597 (ttt) cc_final: 0.7161 (mtp) REVERT: D 957 MET cc_start: 0.9438 (ttp) cc_final: 0.9029 (ptm) REVERT: D 1102 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8671 (mt) REVERT: D 1105 MET cc_start: 0.7899 (tpp) cc_final: 0.7592 (tpp) REVERT: D 1288 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.6067 (m-80) REVERT: D 1342 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8498 (mm) REVERT: D 1522 MET cc_start: 0.9181 (mmm) cc_final: 0.8757 (tpp) REVERT: D 1549 MET cc_start: 0.7542 (mmm) cc_final: 0.6629 (mmm) REVERT: E 45 MET cc_start: 0.7892 (ptm) cc_final: 0.6837 (tmm) REVERT: F 720 TYR cc_start: 0.1934 (OUTLIER) cc_final: 0.1364 (t80) outliers start: 34 outliers final: 16 residues processed: 255 average time/residue: 0.1957 time to fit residues: 82.1367 Evaluate side-chains 222 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 1102 ILE Chi-restraints excluded: chain D residue 1272 GLN Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1288 TYR Chi-restraints excluded: chain D residue 1342 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain F residue 681 LEU Chi-restraints excluded: chain F residue 720 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 226 optimal weight: 0.6980 chunk 214 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 397 optimal weight: 5.9990 chunk 265 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 249 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 32 optimal weight: 0.0470 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 171 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN A1531 ASN ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 743 ASN ** D 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 ASN D1531 ASN ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.077464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.057928 restraints weight = 315762.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.058017 restraints weight = 206526.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.057487 restraints weight = 145013.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.057498 restraints weight = 112993.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.057886 restraints weight = 111680.598| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33556 Z= 0.142 Angle : 0.701 13.161 45324 Z= 0.361 Chirality : 0.045 0.286 5024 Planarity : 0.005 0.071 5796 Dihedral : 5.803 33.741 4394 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 1.53 % Allowed : 13.76 % Favored : 84.71 % 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 are not related in a simple way. whole: -2.09 (0.13), residues: 4022 helix: -0.44 (0.11), residues: 1878 sheet: -1.85 (0.29), residues: 276 loop : -2.33 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1208 TYR 0.017 0.001 TYR A 969 PHE 0.016 0.001 PHE A 798 TRP 0.018 0.002 TRP B 56 HIS 0.008 0.001 HIS D 154 Details of bonding type rmsd covalent geometry : bond 0.00306 (33556) covalent geometry : angle 0.70072 (45324) hydrogen bonds : bond 0.04745 ( 1444) hydrogen bonds : angle 5.76644 ( 4230) *********************** 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 268 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.3842 (mtt) cc_final: 0.3519 (pmm) REVERT: A 431 MET cc_start: 0.8758 (tpt) cc_final: 0.8282 (mmt) REVERT: A 658 MET cc_start: 0.6724 (tpp) cc_final: 0.6366 (tpp) REVERT: A 925 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9113 (mm) REVERT: A 943 MET cc_start: 0.3954 (ttt) cc_final: 0.2893 (ptm) REVERT: A 957 MET cc_start: 0.9428 (ttp) cc_final: 0.9002 (ptm) REVERT: A 1060 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8233 (tp-100) REVERT: A 1064 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8569 (m-10) REVERT: A 1102 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8762 (mt) REVERT: A 1221 MET cc_start: 0.8604 (mtt) cc_final: 0.8372 (mmt) REVERT: A 1522 MET cc_start: 0.9111 (mmm) cc_final: 0.8645 (tpp) REVERT: A 1549 MET cc_start: 0.7692 (mmm) cc_final: 0.7073 (mmm) REVERT: B 1 MET cc_start: 0.5820 (tpt) cc_final: 0.5496 (tpt) REVERT: B 45 MET cc_start: 0.8205 (ptm) cc_final: 0.7740 (tmm) REVERT: C 720 TYR cc_start: 0.2145 (OUTLIER) cc_final: 0.1496 (t80) REVERT: D 120 MET cc_start: 0.8801 (mmt) cc_final: 0.8559 (mmt) REVERT: D 306 MET cc_start: -0.4726 (pmm) cc_final: -0.5419 (ptm) REVERT: D 364 MET cc_start: 0.3614 (mtt) cc_final: 0.3311 (pmm) REVERT: D 658 MET cc_start: 0.6622 (tpp) cc_final: 0.6329 (tpp) REVERT: D 681 MET cc_start: 0.5302 (tmm) cc_final: 0.4724 (mmm) REVERT: D 683 MET cc_start: 0.7641 (ttt) cc_final: 0.7269 (ppp) REVERT: D 741 VAL cc_start: 0.2324 (OUTLIER) cc_final: 0.1907 (t) REVERT: D 957 MET cc_start: 0.9410 (ttp) cc_final: 0.9054 (ptm) REVERT: D 1102 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8676 (mt) REVERT: D 1105 MET cc_start: 0.8383 (tpp) cc_final: 0.7957 (tpp) REVERT: D 1288 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.6160 (m-80) REVERT: D 1522 MET cc_start: 0.9150 (mmm) cc_final: 0.8643 (tpp) REVERT: D 1549 MET cc_start: 0.7571 (mmm) cc_final: 0.6798 (mmm) REVERT: E 1 MET cc_start: 0.5940 (tpt) cc_final: 0.5571 (tpt) REVERT: E 45 MET cc_start: 0.7967 (ptm) cc_final: 0.7352 (tmm) REVERT: F 720 TYR cc_start: 0.2234 (OUTLIER) cc_final: 0.1662 (t80) outliers start: 56 outliers final: 23 residues processed: 259 average time/residue: 0.1850 time to fit residues: 80.9382 Evaluate side-chains 224 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 1064 PHE Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 1102 ILE Chi-restraints excluded: chain D residue 1112 VAL Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1288 TYR Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain D residue 1520 GLU Chi-restraints excluded: chain F residue 681 LEU Chi-restraints excluded: chain F residue 720 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 369 optimal weight: 7.9990 chunk 269 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 233 optimal weight: 50.0000 chunk 44 optimal weight: 30.0000 chunk 317 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 338 optimal weight: 8.9990 chunk 385 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1219 ASN A1401 GLN ** A1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1535 GLN ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1596 GLN ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 ASN D 250 GLN ** D 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 937 ASN D 971 HIS ** D1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1219 ASN D1401 GLN ** D1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1535 GLN ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.068365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.044659 restraints weight = 221470.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.045194 restraints weight = 167665.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.045382 restraints weight = 142396.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.045737 restraints weight = 129178.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.045850 restraints weight = 120144.866| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 33556 Z= 0.329 Angle : 0.859 11.764 45324 Z= 0.450 Chirality : 0.049 0.280 5024 Planarity : 0.006 0.065 5796 Dihedral : 6.121 39.676 4394 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 29.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 2.87 % Allowed : 16.03 % Favored : 81.10 % 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 are not related in a simple way. whole: -2.56 (0.12), residues: 4022 helix: -0.96 (0.11), residues: 1876 sheet: -2.19 (0.30), residues: 234 loop : -2.39 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 102 TYR 0.022 0.003 TYR D 258 PHE 0.031 0.003 PHE D1308 TRP 0.016 0.002 TRP A1006 HIS 0.029 0.002 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00689 (33556) covalent geometry : angle 0.85899 (45324) hydrogen bonds : bond 0.05637 ( 1444) hydrogen bonds : angle 6.24185 ( 4230) *********************** 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 290 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 185 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.4138 (mtt) cc_final: 0.3875 (pmm) REVERT: A 431 MET cc_start: 0.8761 (tpt) cc_final: 0.8116 (mmt) REVERT: A 658 MET cc_start: 0.7127 (tpp) cc_final: 0.6790 (tpp) REVERT: A 683 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7783 (mmp) REVERT: A 925 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9230 (mm) REVERT: A 964 MET cc_start: 0.7585 (ptm) cc_final: 0.7159 (ptm) REVERT: A 1064 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8779 (m-10) REVERT: A 1102 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.7700 (mt) REVERT: A 1549 MET cc_start: 0.8690 (mmm) cc_final: 0.8046 (mmm) REVERT: B 1 MET cc_start: 0.7184 (tpt) cc_final: 0.6979 (tpt) REVERT: B 45 MET cc_start: 0.8512 (ptm) cc_final: 0.8055 (ppp) REVERT: D 96 ARG cc_start: 0.9472 (mtp85) cc_final: 0.9261 (ttp-170) REVERT: D 120 MET cc_start: 0.8896 (mmt) cc_final: 0.8666 (mmt) REVERT: D 364 MET cc_start: 0.3869 (mtt) cc_final: 0.3587 (pmm) REVERT: D 681 MET cc_start: 0.5589 (tmm) cc_final: 0.4834 (mmt) REVERT: D 683 MET cc_start: 0.7749 (ttt) cc_final: 0.7289 (mtp) REVERT: D 964 MET cc_start: 0.8614 (ptm) cc_final: 0.8307 (ptm) REVERT: D 1549 MET cc_start: 0.8553 (mmm) cc_final: 0.7905 (mmm) REVERT: E 1 MET cc_start: 0.7310 (tpt) cc_final: 0.7075 (tpt) outliers start: 105 outliers final: 61 residues processed: 269 average time/residue: 0.1851 time to fit residues: 84.7322 Evaluate side-chains 237 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 172 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1064 PHE Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 711 HIS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 957 MET Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1065 SER Chi-restraints excluded: chain D residue 1112 VAL Chi-restraints excluded: chain D residue 1148 GLU Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1396 LEU Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1491 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain D residue 1520 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 681 LEU Chi-restraints excluded: chain F residue 720 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 76 optimal weight: 8.9990 chunk 200 optimal weight: 20.0000 chunk 28 optimal weight: 40.0000 chunk 391 optimal weight: 6.9990 chunk 298 optimal weight: 0.9980 chunk 300 optimal weight: 0.5980 chunk 190 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 HIS ** D 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 743 ASN D 971 HIS ** D1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1535 GLN ** D1536 HIS ** 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 = 0.4178 r_free = 0.4178 target = 0.069499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.045143 restraints weight = 211753.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.045685 restraints weight = 155750.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.045852 restraints weight = 128562.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.046221 restraints weight = 114007.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.046221 restraints weight = 106563.833| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 33556 Z= 0.211 Angle : 0.734 10.920 45324 Z= 0.380 Chirality : 0.045 0.267 5024 Planarity : 0.005 0.065 5796 Dihedral : 5.907 35.644 4394 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 3.03 % Allowed : 17.78 % Favored : 79.19 % 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 are not related in a simple way. whole: -2.29 (0.12), residues: 4022 helix: -0.71 (0.11), residues: 1878 sheet: -1.79 (0.28), residues: 292 loop : -2.32 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 96 TYR 0.018 0.002 TYR D 258 PHE 0.016 0.002 PHE A 59 TRP 0.015 0.002 TRP A1538 HIS 0.016 0.001 HIS D 971 Details of bonding type rmsd covalent geometry : bond 0.00451 (33556) covalent geometry : angle 0.73374 (45324) hydrogen bonds : bond 0.04897 ( 1444) hydrogen bonds : angle 5.93828 ( 4230) *********************** 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 293 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 182 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7759 (tpp) cc_final: 0.7485 (tpp) REVERT: A 364 MET cc_start: 0.4298 (mtt) cc_final: 0.4077 (pmm) REVERT: A 431 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8263 (mmt) REVERT: A 658 MET cc_start: 0.7165 (tpp) cc_final: 0.6878 (tpp) REVERT: A 683 MET cc_start: 0.8002 (tpp) cc_final: 0.7634 (mmp) REVERT: A 737 LEU cc_start: -0.1714 (OUTLIER) cc_final: -0.1950 (mp) REVERT: A 957 MET cc_start: 0.9412 (ttp) cc_final: 0.9070 (ptp) REVERT: A 964 MET cc_start: 0.7682 (ptm) cc_final: 0.7197 (ptm) REVERT: A 1060 GLN cc_start: 0.8845 (tp-100) cc_final: 0.8489 (tp-100) REVERT: A 1064 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8759 (m-10) REVERT: A 1102 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8541 (mp) REVERT: A 1221 MET cc_start: 0.8917 (mtt) cc_final: 0.8602 (mmt) REVERT: A 1549 MET cc_start: 0.8723 (mmm) cc_final: 0.8084 (mmm) REVERT: B 1 MET cc_start: 0.7006 (tpt) cc_final: 0.6687 (tpt) REVERT: D 117 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8969 (tt) REVERT: D 120 MET cc_start: 0.8882 (mmt) cc_final: 0.8643 (mmt) REVERT: D 681 MET cc_start: 0.5475 (tmm) cc_final: 0.4930 (mmt) REVERT: D 1549 MET cc_start: 0.8632 (mmm) cc_final: 0.7945 (mmm) REVERT: E 1 MET cc_start: 0.7189 (tpt) cc_final: 0.6925 (tpt) outliers start: 111 outliers final: 64 residues processed: 283 average time/residue: 0.1706 time to fit residues: 83.6815 Evaluate side-chains 243 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 174 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 1064 PHE Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 711 HIS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 931 ARG Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 1112 VAL Chi-restraints excluded: chain D residue 1147 PHE Chi-restraints excluded: chain D residue 1148 GLU Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1396 LEU Chi-restraints excluded: chain D residue 1398 LEU Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 681 LEU Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 720 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 335 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 344 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 334 optimal weight: 0.6980 chunk 313 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 358 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1535 GLN ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.069273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.045191 restraints weight = 210348.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.045644 restraints weight = 155656.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.046015 restraints weight = 127476.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.046049 restraints weight = 110981.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.046092 restraints weight = 105244.277| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33556 Z= 0.199 Angle : 0.737 10.856 45324 Z= 0.379 Chirality : 0.046 0.323 5024 Planarity : 0.005 0.065 5796 Dihedral : 5.828 35.530 4394 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 3.17 % Allowed : 19.17 % Favored : 77.66 % 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 are not related in a simple way. whole: -2.17 (0.12), residues: 4022 helix: -0.63 (0.11), residues: 1884 sheet: -1.63 (0.29), residues: 280 loop : -2.25 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1121 TYR 0.017 0.002 TYR D 258 PHE 0.016 0.001 PHE A 59 TRP 0.015 0.002 TRP A1538 HIS 0.016 0.001 HIS D 971 Details of bonding type rmsd covalent geometry : bond 0.00422 (33556) covalent geometry : angle 0.73695 (45324) hydrogen bonds : bond 0.04749 ( 1444) hydrogen bonds : angle 5.89606 ( 4230) *********************** 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 291 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 175 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7819 (tpp) cc_final: 0.7585 (tpp) REVERT: A 364 MET cc_start: 0.4350 (mtt) cc_final: 0.4122 (pmm) REVERT: A 431 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8312 (mmt) REVERT: A 658 MET cc_start: 0.7186 (tpp) cc_final: 0.6884 (tpp) REVERT: A 669 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7893 (tt) REVERT: A 681 MET cc_start: 0.4127 (tpp) cc_final: 0.1809 (mmt) REVERT: A 943 MET cc_start: 0.4539 (ttt) cc_final: 0.3475 (ptm) REVERT: A 1009 MET cc_start: 0.8674 (tpt) cc_final: 0.8413 (tpt) REVERT: A 1060 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8477 (tp-100) REVERT: A 1064 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8690 (m-10) REVERT: A 1102 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8532 (mt) REVERT: A 1221 MET cc_start: 0.8961 (mtt) cc_final: 0.8638 (mmt) REVERT: A 1406 GLU cc_start: 0.5834 (OUTLIER) cc_final: 0.4748 (pm20) REVERT: A 1549 MET cc_start: 0.8804 (mmm) cc_final: 0.8404 (mmm) REVERT: B 1 MET cc_start: 0.7047 (tpt) cc_final: 0.6706 (tpt) REVERT: D 117 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8979 (tt) REVERT: D 120 MET cc_start: 0.8909 (mmt) cc_final: 0.8681 (mmt) REVERT: D 681 MET cc_start: 0.5729 (tmm) cc_final: 0.5246 (mmt) REVERT: D 964 MET cc_start: 0.8580 (ptm) cc_final: 0.7925 (ppp) REVERT: D 1406 GLU cc_start: 0.6003 (OUTLIER) cc_final: 0.3524 (pp20) REVERT: D 1449 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6815 (mp10) REVERT: D 1549 MET cc_start: 0.8698 (mmm) cc_final: 0.8010 (mmm) REVERT: E 1 MET cc_start: 0.7271 (tpt) cc_final: 0.6974 (tpt) outliers start: 116 outliers final: 79 residues processed: 281 average time/residue: 0.1765 time to fit residues: 85.5625 Evaluate side-chains 260 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 173 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1064 PHE Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1147 PHE Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1328 TYR Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 711 HIS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 899 HIS Chi-restraints excluded: chain D residue 931 ARG Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1112 VAL Chi-restraints excluded: chain D residue 1147 PHE Chi-restraints excluded: chain D residue 1148 GLU Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1221 MET Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1342 LEU Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1356 MET Chi-restraints excluded: chain D residue 1396 LEU Chi-restraints excluded: chain D residue 1398 LEU Chi-restraints excluded: chain D residue 1406 GLU Chi-restraints excluded: chain D residue 1449 GLN Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1491 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 681 LEU Chi-restraints excluded: chain F residue 698 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 222 optimal weight: 0.0030 chunk 373 optimal weight: 6.9990 chunk 397 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 385 optimal weight: 5.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS A 653 ASN ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 HIS D 605 ASN ** D 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.068756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.044653 restraints weight = 216010.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.045911 restraints weight = 170108.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.045652 restraints weight = 114180.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.045467 restraints weight = 115845.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.045423 restraints weight = 115969.197| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33556 Z= 0.200 Angle : 0.742 12.655 45324 Z= 0.381 Chirality : 0.046 0.355 5024 Planarity : 0.005 0.064 5796 Dihedral : 5.780 34.598 4394 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 3.41 % Allowed : 19.14 % Favored : 77.44 % 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 are not related in a simple way. whole: -2.12 (0.13), residues: 4022 helix: -0.61 (0.11), residues: 1888 sheet: -1.70 (0.30), residues: 264 loop : -2.20 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1121 TYR 0.030 0.002 TYR A 972 PHE 0.014 0.001 PHE D 59 TRP 0.045 0.002 TRP D1091 HIS 0.037 0.001 HIS A 971 Details of bonding type rmsd covalent geometry : bond 0.00426 (33556) covalent geometry : angle 0.74250 (45324) hydrogen bonds : bond 0.04705 ( 1444) hydrogen bonds : angle 5.86796 ( 4230) *********************** 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 301 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 176 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.4335 (mtt) cc_final: 0.4114 (pmm) REVERT: A 431 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8375 (mmt) REVERT: A 683 MET cc_start: 0.8075 (tpt) cc_final: 0.7643 (tmm) REVERT: A 957 MET cc_start: 0.9334 (ttp) cc_final: 0.9063 (ptp) REVERT: A 1060 GLN cc_start: 0.8861 (tp-100) cc_final: 0.8488 (tp-100) REVERT: A 1064 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8565 (m-10) REVERT: A 1079 MET cc_start: 0.8724 (pmm) cc_final: 0.8268 (pmm) REVERT: A 1102 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8502 (mt) REVERT: A 1221 MET cc_start: 0.8951 (mtt) cc_final: 0.8628 (mmt) REVERT: A 1406 GLU cc_start: 0.5967 (OUTLIER) cc_final: 0.3151 (pm20) REVERT: A 1522 MET cc_start: 0.9176 (mtp) cc_final: 0.8715 (ttp) REVERT: A 1549 MET cc_start: 0.8837 (mmm) cc_final: 0.8289 (mmm) REVERT: B 1 MET cc_start: 0.7265 (tpt) cc_final: 0.6982 (tpt) REVERT: D 117 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9021 (tt) REVERT: D 120 MET cc_start: 0.8829 (mmt) cc_final: 0.8614 (mmt) REVERT: D 964 MET cc_start: 0.8577 (ptm) cc_final: 0.7996 (ppp) REVERT: D 1060 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8579 (tp-100) REVERT: D 1079 MET cc_start: 0.8599 (pmm) cc_final: 0.8151 (pmm) REVERT: D 1406 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.3498 (pp20) REVERT: D 1449 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.6887 (mp10) REVERT: D 1549 MET cc_start: 0.8806 (mmm) cc_final: 0.8160 (mmm) REVERT: E 1 MET cc_start: 0.7254 (tpt) cc_final: 0.6975 (tpt) REVERT: E 45 MET cc_start: 0.8342 (ttt) cc_final: 0.8030 (ttt) outliers start: 125 outliers final: 88 residues processed: 289 average time/residue: 0.1771 time to fit residues: 87.3035 Evaluate side-chains 266 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 171 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1064 PHE Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1147 PHE Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1328 TYR Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 400 TRP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 711 HIS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 899 HIS Chi-restraints excluded: chain D residue 931 ARG Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1112 VAL Chi-restraints excluded: chain D residue 1127 ILE Chi-restraints excluded: chain D residue 1146 MET Chi-restraints excluded: chain D residue 1147 PHE Chi-restraints excluded: chain D residue 1148 GLU Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1221 MET Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1288 TYR Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1342 LEU Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1356 MET Chi-restraints excluded: chain D residue 1396 LEU Chi-restraints excluded: chain D residue 1398 LEU Chi-restraints excluded: chain D residue 1406 GLU Chi-restraints excluded: chain D residue 1449 GLN Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1491 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 681 LEU Chi-restraints excluded: chain F residue 698 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 285 optimal weight: 0.9990 chunk 377 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 393 optimal weight: 8.9990 chunk 137 optimal weight: 0.9990 chunk 216 optimal weight: 7.9990 chunk 223 optimal weight: 30.0000 chunk 386 optimal weight: 0.1980 chunk 247 optimal weight: 20.0000 chunk 261 optimal weight: 50.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 GLN D 314 HIS D 653 ASN ** D 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.067469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.044355 restraints weight = 208306.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.044818 restraints weight = 153523.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.044999 restraints weight = 130397.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.045168 restraints weight = 116755.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.045218 restraints weight = 110037.939| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 33556 Z= 0.229 Angle : 0.766 10.915 45324 Z= 0.395 Chirality : 0.047 0.356 5024 Planarity : 0.005 0.064 5796 Dihedral : 5.821 35.840 4394 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 2.95 % Allowed : 20.15 % Favored : 76.90 % 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 are not related in a simple way. whole: -2.17 (0.13), residues: 4022 helix: -0.68 (0.11), residues: 1912 sheet: -1.49 (0.30), residues: 280 loop : -2.24 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 804 TYR 0.026 0.002 TYR A 972 PHE 0.024 0.002 PHE D1064 TRP 0.075 0.002 TRP D1091 HIS 0.009 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00486 (33556) covalent geometry : angle 0.76619 (45324) hydrogen bonds : bond 0.04846 ( 1444) hydrogen bonds : angle 5.94952 ( 4230) *********************** 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 280 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 172 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.4486 (mtt) cc_final: 0.4280 (pmm) REVERT: A 431 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8242 (mmt) REVERT: A 681 MET cc_start: 0.4056 (tpt) cc_final: 0.1705 (mmt) REVERT: A 683 MET cc_start: 0.7951 (tpt) cc_final: 0.7396 (tmm) REVERT: A 943 MET cc_start: 0.4320 (ttt) cc_final: 0.4051 (ptm) REVERT: A 957 MET cc_start: 0.9320 (ttp) cc_final: 0.9035 (ptp) REVERT: A 1060 GLN cc_start: 0.8795 (tp-100) cc_final: 0.8449 (tp-100) REVERT: A 1064 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8544 (m-10) REVERT: A 1079 MET cc_start: 0.8628 (pmm) cc_final: 0.8371 (pmm) REVERT: A 1102 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8487 (mt) REVERT: A 1406 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.3531 (pm20) REVERT: A 1522 MET cc_start: 0.9248 (mtp) cc_final: 0.8772 (ttp) REVERT: A 1549 MET cc_start: 0.8983 (mmm) cc_final: 0.8406 (mmm) REVERT: B 1 MET cc_start: 0.7268 (tpt) cc_final: 0.6998 (tpt) REVERT: D 105 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7618 (mt) REVERT: D 117 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9045 (tt) REVERT: D 120 MET cc_start: 0.8849 (mmt) cc_final: 0.8606 (mmt) REVERT: D 681 MET cc_start: 0.5067 (tpt) cc_final: 0.2664 (mmt) REVERT: D 683 MET cc_start: 0.7750 (ttt) cc_final: 0.7235 (mtp) REVERT: D 964 MET cc_start: 0.8433 (ptm) cc_final: 0.7539 (ppp) REVERT: D 1079 MET cc_start: 0.8570 (pmm) cc_final: 0.8143 (pmm) REVERT: D 1406 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.3509 (pp20) REVERT: D 1449 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6959 (mp10) REVERT: D 1549 MET cc_start: 0.8939 (mmm) cc_final: 0.8259 (mmm) REVERT: E 1 MET cc_start: 0.7267 (tpt) cc_final: 0.6979 (tpt) REVERT: E 45 MET cc_start: 0.8439 (ttt) cc_final: 0.8158 (ttt) outliers start: 108 outliers final: 83 residues processed: 268 average time/residue: 0.1768 time to fit residues: 81.6317 Evaluate side-chains 261 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 170 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 1064 PHE Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1147 PHE Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1328 TYR Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 400 TRP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 711 HIS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 899 HIS Chi-restraints excluded: chain D residue 931 ARG Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1112 VAL Chi-restraints excluded: chain D residue 1146 MET Chi-restraints excluded: chain D residue 1147 PHE Chi-restraints excluded: chain D residue 1148 GLU Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1221 MET Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1288 TYR Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1342 LEU Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1356 MET Chi-restraints excluded: chain D residue 1396 LEU Chi-restraints excluded: chain D residue 1398 LEU Chi-restraints excluded: chain D residue 1406 GLU Chi-restraints excluded: chain D residue 1449 GLN Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1491 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 681 LEU Chi-restraints excluded: chain F residue 698 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 120 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 393 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 364 optimal weight: 20.0000 chunk 302 optimal weight: 6.9990 chunk 363 optimal weight: 3.9990 chunk 288 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 312 optimal weight: 0.0870 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 HIS ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 HIS ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.070340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.044380 restraints weight = 215841.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.044921 restraints weight = 154018.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.045297 restraints weight = 125803.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.045504 restraints weight = 111492.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.045659 restraints weight = 103801.146| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33556 Z= 0.145 Angle : 0.733 12.331 45324 Z= 0.371 Chirality : 0.045 0.401 5024 Planarity : 0.005 0.060 5796 Dihedral : 5.637 33.496 4394 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 2.08 % Allowed : 21.05 % Favored : 76.87 % 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 are not related in a simple way. whole: -1.95 (0.13), residues: 4022 helix: -0.46 (0.11), residues: 1928 sheet: -1.43 (0.30), residues: 292 loop : -2.18 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1088 TYR 0.016 0.001 TYR D 819 PHE 0.025 0.001 PHE D1064 TRP 0.066 0.002 TRP D1091 HIS 0.008 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00314 (33556) covalent geometry : angle 0.73299 (45324) hydrogen bonds : bond 0.04437 ( 1444) hydrogen bonds : angle 5.72855 ( 4230) *********************** 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 258 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 182 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.4461 (mtt) cc_final: 0.4239 (pmm) REVERT: A 431 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8315 (mmp) REVERT: A 681 MET cc_start: 0.3778 (tpt) cc_final: 0.1591 (mmt) REVERT: A 683 MET cc_start: 0.7854 (tpt) cc_final: 0.7288 (tmm) REVERT: A 802 MET cc_start: 0.8729 (mmt) cc_final: 0.8473 (mmt) REVERT: A 957 MET cc_start: 0.9297 (ttp) cc_final: 0.9042 (ptp) REVERT: A 1060 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8481 (tp-100) REVERT: A 1064 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8562 (m-10) REVERT: A 1102 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8578 (mt) REVERT: A 1221 MET cc_start: 0.8872 (mtt) cc_final: 0.8379 (mmp) REVERT: A 1522 MET cc_start: 0.9235 (mtp) cc_final: 0.8729 (ttp) REVERT: A 1549 MET cc_start: 0.8911 (mmm) cc_final: 0.8335 (mmm) REVERT: B 1 MET cc_start: 0.7041 (tpt) cc_final: 0.6745 (tpt) REVERT: D 105 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7601 (mt) REVERT: D 117 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9027 (tt) REVERT: D 120 MET cc_start: 0.8783 (mmt) cc_final: 0.8558 (mmt) REVERT: D 681 MET cc_start: 0.4867 (tpt) cc_final: 0.2605 (mmt) REVERT: D 964 MET cc_start: 0.8518 (ptm) cc_final: 0.7945 (ppp) REVERT: D 1079 MET cc_start: 0.8580 (pmm) cc_final: 0.8273 (pmm) REVERT: D 1288 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6525 (m-80) REVERT: D 1549 MET cc_start: 0.8867 (mmm) cc_final: 0.8223 (mmm) REVERT: E 45 MET cc_start: 0.8334 (ttt) cc_final: 0.8110 (ttt) outliers start: 76 outliers final: 59 residues processed: 251 average time/residue: 0.1746 time to fit residues: 75.5027 Evaluate side-chains 242 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 177 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1064 PHE Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1328 TYR Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 400 TRP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 711 HIS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 931 ARG Chi-restraints excluded: chain D residue 1146 MET Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1288 TYR Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1342 LEU Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1396 LEU Chi-restraints excluded: chain D residue 1449 GLN Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain E residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 272 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 385 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 389 optimal weight: 0.0270 chunk 364 optimal weight: 0.1980 chunk 216 optimal weight: 1.9990 chunk 188 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 overall best weight: 2.2444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.069328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.044546 restraints weight = 215101.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.045216 restraints weight = 166526.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.045104 restraints weight = 129288.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.045039 restraints weight = 132246.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.045080 restraints weight = 127829.886| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33556 Z= 0.169 Angle : 0.738 12.324 45324 Z= 0.375 Chirality : 0.046 0.406 5024 Planarity : 0.005 0.062 5796 Dihedral : 5.579 34.652 4394 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.88 % Allowed : 21.05 % Favored : 77.06 % 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 are not related in a simple way. whole: -1.89 (0.13), residues: 4022 helix: -0.42 (0.11), residues: 1910 sheet: -1.35 (0.31), residues: 292 loop : -2.15 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 804 TYR 0.017 0.001 TYR F 720 PHE 0.025 0.001 PHE D 798 TRP 0.060 0.002 TRP D1091 HIS 0.008 0.001 HIS D 899 Details of bonding type rmsd covalent geometry : bond 0.00367 (33556) covalent geometry : angle 0.73835 (45324) hydrogen bonds : bond 0.04431 ( 1444) hydrogen bonds : angle 5.76114 ( 4230) ********************** 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 246 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 177 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.4485 (mtt) cc_final: 0.4263 (pmm) REVERT: A 431 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8456 (mmp) REVERT: A 681 MET cc_start: 0.3847 (tpt) cc_final: 0.1619 (mmt) REVERT: A 683 MET cc_start: 0.7889 (tpt) cc_final: 0.7299 (tmm) REVERT: A 1132 MET cc_start: 0.8116 (ppp) cc_final: 0.7224 (ppp) REVERT: A 1221 MET cc_start: 0.8805 (mtt) cc_final: 0.8526 (mmt) REVERT: A 1549 MET cc_start: 0.8961 (mmm) cc_final: 0.8336 (mmm) REVERT: B 1 MET cc_start: 0.7081 (tpt) cc_final: 0.6779 (tpt) REVERT: D 1 MET cc_start: 0.2688 (tpp) cc_final: 0.2059 (tpp) REVERT: D 120 MET cc_start: 0.8838 (mmt) cc_final: 0.8588 (mmt) REVERT: D 681 MET cc_start: 0.4867 (tpt) cc_final: 0.2684 (mmt) REVERT: D 683 MET cc_start: 0.7762 (ttt) cc_final: 0.7366 (tmm) REVERT: D 964 MET cc_start: 0.8433 (ptm) cc_final: 0.7888 (ppp) REVERT: D 1132 MET cc_start: 0.8201 (ppp) cc_final: 0.7967 (ppp) REVERT: D 1288 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: D 1549 MET cc_start: 0.8929 (mmm) cc_final: 0.8276 (mmm) outliers start: 69 outliers final: 63 residues processed: 240 average time/residue: 0.1766 time to fit residues: 73.0947 Evaluate side-chains 240 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 175 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1147 PHE Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1328 TYR Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 400 TRP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 711 HIS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 931 ARG Chi-restraints excluded: chain D residue 1146 MET Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1221 MET Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1288 TYR Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1342 LEU Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1396 LEU Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 698 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 350 optimal weight: 0.9980 chunk 40 optimal weight: 30.0000 chunk 293 optimal weight: 0.9990 chunk 282 optimal weight: 0.0010 chunk 105 optimal weight: 7.9990 chunk 326 optimal weight: 0.9980 chunk 358 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 377 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** A1404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1614 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.071252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.044490 restraints weight = 227745.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.045105 restraints weight = 160183.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.045484 restraints weight = 129728.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.045706 restraints weight = 113196.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.045942 restraints weight = 105157.460| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33556 Z= 0.134 Angle : 0.740 13.283 45324 Z= 0.371 Chirality : 0.045 0.309 5024 Planarity : 0.004 0.059 5796 Dihedral : 5.472 32.573 4394 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 1.75 % Allowed : 21.33 % Favored : 76.93 % 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 are not related in a simple way. whole: -1.80 (0.13), residues: 4022 helix: -0.31 (0.11), residues: 1932 sheet: -1.42 (0.31), residues: 276 loop : -2.14 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.015 0.001 TYR C 720 PHE 0.034 0.001 PHE D 798 TRP 0.058 0.002 TRP D1091 HIS 0.008 0.001 HIS D 899 Details of bonding type rmsd covalent geometry : bond 0.00291 (33556) covalent geometry : angle 0.74000 (45324) hydrogen bonds : bond 0.04237 ( 1444) hydrogen bonds : angle 5.63091 ( 4230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9995.22 seconds wall clock time: 171 minutes 44.44 seconds (10304.44 seconds total)