Starting phenix.real_space_refine on Mon Sep 14 20:46:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vba_31876/09_2026/7vba_31876_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vba_31876/09_2026/7vba_31876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vba_31876/09_2026/7vba_31876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vba_31876/09_2026/7vba_31876.map" model { file = "/net/cci-nas-00/data/ceres_data/7vba_31876/09_2026/7vba_31876_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vba_31876/09_2026/7vba_31876_neut_trim.cif" } resolution = 2.89 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= -0.002 sd= 0.151 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 44 5.49 5 Mg 1 5.21 5 S 220 5.16 5 C 20865 2.51 5 N 5767 2.21 5 O 6177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33079 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1473, 11749 Classifications: {'peptide': 1473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 71, 'TRANS': 1401} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8912 Classifications: {'peptide': 1123} Link IDs: {'PTRANS': 63, 'TRANS': 1059} Chain breaks: 1 Chain: "C" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2697 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain: "E" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1641 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 10, 'TRANS': 188} Chain breaks: 1 Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "H" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1176 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "I" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 447 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 863 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 379 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "N" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1105 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 24, 'TRANS': 126} Chain: "G" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1229 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "M" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 867 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "R" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 5} Link IDs: {'rna3p': 7} Chain: "T" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 456 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "U" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 238 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 1, ' ZN': 2, '2TM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 455 SG CYS A 64 60.563 56.328 58.882 1.00 70.96 S ATOM 474 SG CYS A 67 63.144 55.957 56.706 1.00 70.13 S ATOM 529 SG CYS A 74 62.920 57.836 60.489 1.00 63.65 S ATOM 767 SG CYS A 104 63.181 108.926 50.085 1.00 76.34 S ATOM 789 SG CYS A 107 64.340 109.379 46.745 1.00 82.67 S ATOM 1491 SG CYS A 205 66.268 111.265 49.614 1.00 87.17 S ATOM 20214 SG CYS B1070 75.151 66.247 49.271 1.00 51.70 S ATOM 20236 SG CYS B1073 73.880 69.240 48.145 1.00 54.67 S ATOM 20370 SG CYS B1098 71.599 66.222 48.929 1.00 72.84 S ATOM 20391 SG CYS B1101 73.406 66.995 45.360 1.00 83.89 S ATOM 27287 SG CYS J 7 77.049 45.364 128.555 1.00 34.15 S ATOM 27311 SG CYS J 10 79.902 42.644 130.073 1.00 21.98 S ATOM 27575 SG CYS J 44 80.106 46.624 130.501 1.00 21.89 S ATOM 27581 SG CYS J 45 78.026 44.410 132.565 1.00 24.31 S ATOM 28651 SG CYS L 19 35.893 46.649 111.648 1.00 40.38 S ATOM 28787 SG CYS L 36 33.517 44.676 110.069 1.00 44.67 S ATOM 28813 SG CYS L 39 32.454 47.099 111.952 1.00 47.99 S Residues with excluded nonbonded symmetry interactions: 161 residue: pdb=" N GLY N 127 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 127 " occ=0.00 residue: pdb=" N GLY N 144 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 144 " occ=0.00 residue: pdb=" N GLY N 153 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 153 " occ=0.00 residue: pdb=" N GLY N 154 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 154 " occ=0.00 residue: pdb=" N SER G 46 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER G 46 " occ=0.00 residue: pdb=" N CYS G 47 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS G 47 " occ=0.00 residue: pdb=" N LEU G 48 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU G 48 " occ=0.00 residue: pdb=" N VAL G 49 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL G 49 " occ=0.00 residue: pdb=" N ALA G 50 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 50 " occ=0.00 residue: pdb=" N GLY G 51 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY G 51 " occ=0.00 residue: pdb=" N PRO G 52 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO G 52 " occ=0.00 residue: pdb=" N HIS G 53 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS G 53 " occ=0.00 ... (remaining 149 not shown) Time building chain proxies: 6.73, per 1000 atoms: 0.20 Number of scatterers: 33079 At special positions: 0 Unit cell: (155.992, 161.262, 177.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 220 16.00 P 44 15.00 Mg 1 11.99 O 6177 8.00 N 5767 7.00 C 20865 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: 3.41 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 64 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 205 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 107 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 104 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1101 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1073 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1070 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 44 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 7 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 39 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 36 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 19 " Number of angles added : 12 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7576 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 36 sheets defined 33.2% alpha, 12.6% beta 11 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 5.11 Creating SS restraints... Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 132 through 144 removed outlier: 4.668A pdb=" N TYR A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 removed outlier: 4.260A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.956A pdb=" N ALA A 179 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A 180 " --> pdb=" O GLN A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 180' Processing helix chain 'A' and resid 184 through 199 removed outlier: 3.540A pdb=" N LYS A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.700A pdb=" N LYS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 296 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 322 through 348 Processing helix chain 'A' and resid 382 through 401 Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.909A pdb=" N ASP A 407 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.642A pdb=" N LYS A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.830A pdb=" N TYR A 585 " --> pdb=" O ASN A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.785A pdb=" N GLU A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 634 through 642 removed outlier: 3.567A pdb=" N GLY A 638 " --> pdb=" O HIS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 684 through 696 removed outlier: 3.810A pdb=" N ASN A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 removed outlier: 3.654A pdb=" N MET A 732 " --> pdb=" O PRO A 729 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N CYS A 733 " --> pdb=" O ASP A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 770 Processing helix chain 'A' and resid 770 through 792 removed outlier: 3.675A pdb=" N SER A 774 " --> pdb=" O GLY A 770 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 820 removed outlier: 3.608A pdb=" N THR A 820 " --> pdb=" O ILE A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 831 removed outlier: 3.773A pdb=" N ALA A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 851 Processing helix chain 'A' and resid 857 through 881 removed outlier: 3.846A pdb=" N ILE A 861 " --> pdb=" O ASP A 857 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 868 " --> pdb=" O LYS A 864 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 910 Processing helix chain 'A' and resid 944 through 948 Processing helix chain 'A' and resid 960 through 996 removed outlier: 3.655A pdb=" N LEU A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1030 removed outlier: 3.614A pdb=" N LYS A1028 " --> pdb=" O ASP A1025 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN A1030 " --> pdb=" O PRO A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1043 Processing helix chain 'A' and resid 1043 through 1051 Processing helix chain 'A' and resid 1052 through 1059 removed outlier: 3.706A pdb=" N VAL A1056 " --> pdb=" O HIS A1052 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A1057 " --> pdb=" O LEU A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1079 Processing helix chain 'A' and resid 1087 through 1092 Processing helix chain 'A' and resid 1095 through 1103 removed outlier: 4.499A pdb=" N ALA A1102 " --> pdb=" O GLU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1126 removed outlier: 4.042A pdb=" N GLN A1118 " --> pdb=" O SER A1114 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU A1119 " --> pdb=" O PRO A1115 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 3.764A pdb=" N ALA A1140 " --> pdb=" O LYS A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.531A pdb=" N VAL A1149 " --> pdb=" O PRO A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1179 removed outlier: 3.800A pdb=" N THR A1165 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A1176 " --> pdb=" O GLN A1172 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A1179 " --> pdb=" O ALA A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1202 removed outlier: 3.949A pdb=" N THR A1194 " --> pdb=" O ASP A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1226 removed outlier: 3.758A pdb=" N LEU A1214 " --> pdb=" O ALA A1210 " (cutoff:3.500A) Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1244 through 1252 Processing helix chain 'A' and resid 1271 through 1286 removed outlier: 3.925A pdb=" N LYS A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A1280 " --> pdb=" O LYS A1276 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A1286 " --> pdb=" O LYS A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1293 No H-bonds generated for 'chain 'A' and resid 1291 through 1293' Processing helix chain 'A' and resid 1323 through 1331 removed outlier: 4.030A pdb=" N TYR A1326 " --> pdb=" O PRO A1323 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A1327 " --> pdb=" O HIS A1324 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLN A1328 " --> pdb=" O ALA A1325 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A1329 " --> pdb=" O TYR A1326 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A1330 " --> pdb=" O TYR A1327 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A1331 " --> pdb=" O GLN A1328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1323 through 1331' Processing helix chain 'A' and resid 1334 through 1345 Processing helix chain 'A' and resid 1345 through 1359 removed outlier: 4.116A pdb=" N MET A1351 " --> pdb=" O PHE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1509 removed outlier: 3.640A pdb=" N ARG A1501 " --> pdb=" O ALA A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1547 Processing helix chain 'A' and resid 1585 through 1592 removed outlier: 4.967A pdb=" N LYS A1590 " --> pdb=" O GLU A1587 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A1592 " --> pdb=" O PHE A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1612 Processing helix chain 'A' and resid 1613 through 1631 removed outlier: 4.247A pdb=" N ARG A1619 " --> pdb=" O GLU A1615 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1620 " --> pdb=" O ALA A1616 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A1631 " --> pdb=" O ASP A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1649 removed outlier: 3.758A pdb=" N LEU A1641 " --> pdb=" O ASP A1637 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A1643 " --> pdb=" O ARG A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1687 Processing helix chain 'A' and resid 1695 through 1702 removed outlier: 3.657A pdb=" N VAL A1702 " --> pdb=" O ALA A1698 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 51 removed outlier: 3.581A pdb=" N SER B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 46 " --> pdb=" O HIS B 42 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 61 removed outlier: 4.003A pdb=" N GLY B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.664A pdb=" N GLU B 158 " --> pdb=" O GLN B 154 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 159' Processing helix chain 'B' and resid 195 through 202 removed outlier: 3.678A pdb=" N LYS B 199 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR B 200 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY B 202 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.830A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 319 through 332 removed outlier: 3.553A pdb=" N ILE B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 358 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 376 through 404 removed outlier: 3.635A pdb=" N GLU B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.561A pdb=" N MET B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 423 removed outlier: 3.666A pdb=" N THR B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 removed outlier: 4.092A pdb=" N PHE B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 431 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 removed outlier: 3.652A pdb=" N TYR B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 removed outlier: 3.662A pdb=" N ALA B 479 " --> pdb=" O ALA B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 538 removed outlier: 3.653A pdb=" N CYS B 535 " --> pdb=" O PRO B 531 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.611A pdb=" N ILE B 640 " --> pdb=" O MET B 637 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE B 641 " --> pdb=" O GLU B 638 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET B 642 " --> pdb=" O GLN B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 637 through 642' Processing helix chain 'B' and resid 676 through 680 removed outlier: 3.560A pdb=" N ASN B 680 " --> pdb=" O SER B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 removed outlier: 3.653A pdb=" N ASN B 685 " --> pdb=" O GLN B 681 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 687 " --> pdb=" O PRO B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 730 Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 800 through 804 removed outlier: 3.837A pdb=" N LEU B 804 " --> pdb=" O PRO B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 924 removed outlier: 3.660A pdb=" N ARG B 923 " --> pdb=" O GLY B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 942 removed outlier: 4.199A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B 933 " --> pdb=" O LEU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 968 Processing helix chain 'B' and resid 1038 through 1046 Processing helix chain 'B' and resid 1050 through 1059 removed outlier: 3.592A pdb=" N LEU B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1125 removed outlier: 3.824A pdb=" N ARG B1117 " --> pdb=" O PRO B1113 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 248 through 256 removed outlier: 3.954A pdb=" N GLU C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 317 through 341 Processing helix chain 'E' and resid 5 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.718A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.937A pdb=" N LYS E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 4.288A pdb=" N ILE E 126 " --> pdb=" O PRO E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 removed outlier: 3.845A pdb=" N THR E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.755A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 48 through 60 Processing helix chain 'K' and resid 93 through 128 removed outlier: 3.658A pdb=" N ASN K 101 " --> pdb=" O GLN K 97 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG K 128 " --> pdb=" O GLN K 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 36 Processing helix chain 'N' and resid 52 through 57 Processing helix chain 'N' and resid 99 through 102 Processing helix chain 'G' and resid 60 through 64 removed outlier: 3.785A pdb=" N LEU G 64 " --> pdb=" O PRO G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 74 removed outlier: 3.801A pdb=" N ARG G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 160 removed outlier: 3.738A pdb=" N GLU G 159 " --> pdb=" O PRO G 156 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN G 160 " --> pdb=" O LYS G 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 156 through 160' Processing helix chain 'M' and resid 35 through 39 removed outlier: 4.147A pdb=" N ASN M 38 " --> pdb=" O SER M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.518A pdb=" N ASN M 82 " --> pdb=" O LEU M 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1690 through 1691 removed outlier: 4.414A pdb=" N GLY A 14 " --> pdb=" O ASP B1133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 88 removed outlier: 10.825A pdb=" N LEU A 83 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N VAL A 303 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N LEU A 85 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE A 301 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.670A pdb=" N THR A 224 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 436 through 437 removed outlier: 4.075A pdb=" N ILE B1035 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 447 removed outlier: 6.041A pdb=" N CYS A 446 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE A 456 " --> pdb=" O ARG A 567 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 471 removed outlier: 4.137A pdb=" N MET A 496 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS A 541 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA A 494 " --> pdb=" O HIS A 541 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 708 Processing sheet with id=AA9, first strand: chain 'A' and resid 917 through 918 Processing sheet with id=AB1, first strand: chain 'A' and resid 1000 through 1001 removed outlier: 6.862A pdb=" N VAL A1007 " --> pdb=" O VAL A1015 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1562 through 1565 removed outlier: 3.686A pdb=" N VAL A1577 " --> pdb=" O ASN A1565 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A1266 " --> pdb=" O LEU A1578 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1288 through 1289 removed outlier: 3.717A pdb=" N VAL A1288 " --> pdb=" O TYR A1554 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A1554 " --> pdb=" O VAL A1288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1526 through 1528 removed outlier: 4.042A pdb=" N GLU I 51 " --> pdb=" O VAL A1299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1713 through 1714 Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 68 removed outlier: 3.530A pdb=" N PHE B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP B 117 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA B 80 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 115 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 82 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS B 113 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 116 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE B 133 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 118 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS B 131 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TRP B 120 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE B 129 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 122 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS B 127 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.506A pdb=" N LEU B 182 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET B 181 " --> pdb=" O CYS B 471 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 190 through 193 removed outlier: 5.363A pdb=" N TYR B 208 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN B 223 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 239 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 519 through 520 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 632 through 635 current: chain 'B' and resid 658 through 660 Processing sheet with id=AC1, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AC2, first strand: chain 'B' and resid 594 through 598 Processing sheet with id=AC3, first strand: chain 'B' and resid 695 through 696 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 695 through 696 current: chain 'B' and resid 913 through 915 removed outlier: 7.461A pdb=" N MET B 757 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 896 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 759 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS B 882 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 712 through 714 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 771 through 780 current: chain 'B' and resid 847 through 855 removed outlier: 7.965A pdb=" N CYS B 847 " --> pdb=" O PRO B 874 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL B 849 " --> pdb=" O ARG B 872 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG B 872 " --> pdb=" O VAL B 849 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN B 851 " --> pdb=" O THR B 870 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N CYS B 866 " --> pdb=" O CYS B 855 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 866 through 874 current: chain 'L' and resid 25 through 26 Processing sheet with id=AC5, first strand: chain 'B' and resid 828 through 830 removed outlier: 3.516A pdb=" N TYR B 828 " --> pdb=" O PHE B 837 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 835 " --> pdb=" O ASN B 830 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1068 through 1070 Processing sheet with id=AC7, first strand: chain 'B' and resid 1079 through 1080 Processing sheet with id=AC8, first strand: chain 'C' and resid 13 through 14 removed outlier: 4.698A pdb=" N LEU C 236 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASP C 304 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N ARG C 234 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 173 through 176 removed outlier: 4.560A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU C 207 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN C 96 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASP C 209 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL C 94 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU C 211 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 92 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 167 through 168 removed outlier: 3.518A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 263 through 265 Processing sheet with id=AD3, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.170A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.523A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.561A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 90 through 91 removed outlier: 5.453A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 27 through 31 Processing sheet with id=AD8, first strand: chain 'N' and resid 18 through 20 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 18 through 20 current: chain 'N' and resid 76 through 85 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 76 through 85 current: chain 'N' and resid 105 through 107 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 105 through 107 current: chain 'M' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 68 through 72 current: chain 'M' and resid 98 through 111 Processing sheet with id=AD9, first strand: chain 'G' and resid 48 through 59 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 48 through 59 current: chain 'G' and resid 112 through 123 No H-bonds generated for sheet with id=AD9 1007 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 9.63 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5404 1.29 - 1.43: 8775 1.43 - 1.56: 19250 1.56 - 1.70: 83 1.70 - 1.84: 343 Bond restraints: 33855 Sorted by residual: bond pdb=" C ARG M 66 " pdb=" N LEU M 67 " ideal model delta sigma weight residual 1.331 1.221 0.110 1.22e-02 6.72e+03 8.09e+01 bond pdb=" C PRO B 590 " pdb=" O PRO B 590 " ideal model delta sigma weight residual 1.246 1.176 0.070 8.50e-03 1.38e+04 6.78e+01 bond pdb=" C ALA M 61 " pdb=" N ALA M 62 " ideal model delta sigma weight residual 1.331 1.227 0.104 1.34e-02 5.57e+03 6.02e+01 bond pdb=" C ASN N 155 " pdb=" N PRO N 156 " ideal model delta sigma weight residual 1.329 1.418 -0.089 1.18e-02 7.18e+03 5.68e+01 bond pdb=" C GLU N 100 " pdb=" N ALA N 101 " ideal model delta sigma weight residual 1.334 1.240 0.093 1.24e-02 6.50e+03 5.65e+01 ... (remaining 33850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 43866 3.33 - 6.66: 1842 6.66 - 9.99: 197 9.99 - 13.32: 38 13.32 - 16.65: 4 Bond angle restraints: 45947 Sorted by residual: angle pdb=" N VAL C 164 " pdb=" CA VAL C 164 " pdb=" C VAL C 164 " ideal model delta sigma weight residual 112.12 98.66 13.46 8.40e-01 1.42e+00 2.57e+02 angle pdb=" N GLU A1507 " pdb=" CA GLU A1507 " pdb=" C GLU A1507 " ideal model delta sigma weight residual 111.07 99.33 11.74 1.07e+00 8.73e-01 1.20e+02 angle pdb=" N THR K 25 " pdb=" CA THR K 25 " pdb=" C THR K 25 " ideal model delta sigma weight residual 113.18 100.87 12.31 1.21e+00 6.83e-01 1.03e+02 angle pdb=" N LEU B 19 " pdb=" CA LEU B 19 " pdb=" C LEU B 19 " ideal model delta sigma weight residual 110.53 97.54 12.99 1.32e+00 5.74e-01 9.68e+01 angle pdb=" N HIS B 159 " pdb=" CA HIS B 159 " pdb=" C HIS B 159 " ideal model delta sigma weight residual 110.32 95.31 15.01 1.59e+00 3.96e-01 8.91e+01 ... (remaining 45942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 19836 35.45 - 70.91: 661 70.91 - 106.36: 34 106.36 - 141.81: 0 141.81 - 177.27: 5 Dihedral angle restraints: 20536 sinusoidal: 8790 harmonic: 11746 Sorted by residual: dihedral pdb=" N GLN A 553 " pdb=" C GLN A 553 " pdb=" CA GLN A 553 " pdb=" CB GLN A 553 " ideal model delta harmonic sigma weight residual 122.80 150.82 -28.02 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" C GLN A 553 " pdb=" N GLN A 553 " pdb=" CA GLN A 553 " pdb=" CB GLN A 553 " ideal model delta harmonic sigma weight residual -122.60 -150.36 27.76 0 2.50e+00 1.60e-01 1.23e+02 dihedral pdb=" C TYR B 730 " pdb=" N TYR B 730 " pdb=" CA TYR B 730 " pdb=" CB TYR B 730 " ideal model delta harmonic sigma weight residual -122.60 -104.21 -18.39 0 2.50e+00 1.60e-01 5.41e+01 ... (remaining 20533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 4909 0.249 - 0.499: 173 0.499 - 0.748: 10 0.748 - 0.997: 0 0.997 - 1.246: 1 Chirality restraints: 5093 Sorted by residual: chirality pdb=" CA GLN A 553 " pdb=" N GLN A 553 " pdb=" C GLN A 553 " pdb=" CB GLN A 553 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.88e+01 chirality pdb=" CA PRO C 259 " pdb=" N PRO C 259 " pdb=" C PRO C 259 " pdb=" CB PRO C 259 " both_signs ideal model delta sigma weight residual False 2.72 1.98 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CB THR K 25 " pdb=" CA THR K 25 " pdb=" OG1 THR K 25 " pdb=" CG2 THR K 25 " both_signs ideal model delta sigma weight residual False 2.55 1.89 0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 5090 not shown) Planarity restraints: 5797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 109 " 0.029 2.00e-02 2.50e+03 5.97e-02 3.56e+01 pdb=" C MET M 109 " -0.103 2.00e-02 2.50e+03 pdb=" O MET M 109 " 0.041 2.00e-02 2.50e+03 pdb=" N GLN M 110 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 14 " 0.027 2.00e-02 2.50e+03 5.33e-02 2.84e+01 pdb=" C ASP H 14 " -0.092 2.00e-02 2.50e+03 pdb=" O ASP H 14 " 0.034 2.00e-02 2.50e+03 pdb=" N ILE H 15 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY N 104 " -0.026 2.00e-02 2.50e+03 5.16e-02 2.67e+01 pdb=" C GLY N 104 " 0.089 2.00e-02 2.50e+03 pdb=" O GLY N 104 " -0.034 2.00e-02 2.50e+03 pdb=" N LEU N 105 " -0.029 2.00e-02 2.50e+03 ... (remaining 5794 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 72 2.39 - 3.02: 19540 3.02 - 3.64: 46980 3.64 - 4.27: 77426 4.27 - 4.90: 129920 Nonbonded interactions: 273938 Sorted by model distance: nonbonded pdb=" O ASP I 16 " pdb=" CD2 LEU M 67 " model vdw 1.758 3.460 nonbonded pdb=" OD1 ASP A 590 " pdb="MG MG A2003 " model vdw 1.982 2.170 nonbonded pdb=" OE1 GLN M 12 " pdb=" NE2 GLN M 98 " model vdw 2.007 3.120 nonbonded pdb=" O3' U R -1 " pdb="MG MG A2003 " model vdw 2.053 2.170 nonbonded pdb=" NZ LYS A 408 " pdb=" CD2 LEU A 409 " model vdw 2.055 3.540 ... (remaining 273933 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 44.570 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.010 0.377 33872 Z= 0.682 Angle : 1.448 21.143 45959 Z= 1.015 Chirality : 0.099 1.246 5093 Planarity : 0.008 0.117 5797 Dihedral : 16.625 177.266 12960 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 27.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.65 % Favored : 91.00 % Rotamer: Outliers : 5.76 % Allowed : 7.20 % Favored : 87.04 % Cbeta Deviations : 2.11 % Peptide Plane: Cis-proline : 0.00 % 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: -3.50 (0.12), residues: 4001 helix: -1.95 (0.13), residues: 1212 sheet: -1.90 (0.19), residues: 646 loop : -2.74 (0.12), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 183 TYR 0.046 0.002 TYR B 826 PHE 0.050 0.002 PHE B 75 TRP 0.029 0.002 TRP A 9 HIS 0.021 0.002 HIS C 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00935 / 0.67 (33855) covalent geometry : angle 1.43577 / 1.01 (45947) hydrogen bonds : bond 0.19389 / 12.61 ( 1035) hydrogen bonds : angle 7.26412 / 5.14 ( 2849) metal coordination : bond 0.14783 / 7.56 ( 17) metal coordination : angle 11.63108 / 7.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 691 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7413 (mtmt) cc_final: 0.7048 (mttm) REVERT: A 91 LEU cc_start: 0.7675 (pt) cc_final: 0.6947 (pt) REVERT: A 172 ASN cc_start: 0.8099 (t0) cc_final: 0.7872 (t0) REVERT: A 200 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8772 (mmp) REVERT: A 204 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6578 (mpp80) REVERT: A 292 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6161 (m-80) REVERT: A 381 GLN cc_start: 0.4624 (OUTLIER) cc_final: 0.3979 (tt0) REVERT: A 407 ASP cc_start: 0.6407 (t0) cc_final: 0.6009 (t70) REVERT: A 411 MET cc_start: 0.7187 (mpp) cc_final: 0.6842 (mpt) REVERT: A 454 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7987 (p0) REVERT: A 465 LYS cc_start: 0.8509 (tttm) cc_final: 0.8255 (tttp) REVERT: A 550 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8370 (mt) REVERT: A 567 ARG cc_start: 0.7542 (tpt90) cc_final: 0.7197 (tpt-90) REVERT: A 635 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7454 (mpp) REVERT: A 1045 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: A 1174 TRP cc_start: 0.7638 (t-100) cc_final: 0.7414 (t60) REVERT: A 1239 MET cc_start: 0.3070 (ptt) cc_final: 0.2458 (mtp) REVERT: A 1263 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7415 (ptm) REVERT: A 1340 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6133 (ttp80) REVERT: A 1714 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 8 ARG cc_start: 0.7203 (mtt180) cc_final: 0.6843 (mmp-170) REVERT: B 20 THR cc_start: 0.8020 (p) cc_final: 0.7793 (p) REVERT: B 32 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7914 (tmtt) REVERT: B 111 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7882 (ptm-80) REVERT: B 131 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7815 (ttmt) REVERT: B 272 LYS cc_start: 0.7847 (mtmt) cc_final: 0.7276 (mtmm) REVERT: B 276 SER cc_start: 0.7619 (OUTLIER) cc_final: 0.7315 (m) REVERT: B 280 ASN cc_start: 0.8239 (m-40) cc_final: 0.8026 (m-40) REVERT: B 321 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: B 325 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: B 327 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7699 (tp) REVERT: B 349 MET cc_start: 0.8048 (mtp) cc_final: 0.7687 (mtp) REVERT: B 422 MET cc_start: 0.4583 (mmm) cc_final: 0.4346 (mmm) REVERT: B 430 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8746 (m-80) REVERT: B 481 MET cc_start: 0.7926 (mtt) cc_final: 0.7551 (mtm) REVERT: B 542 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7220 (pt) REVERT: B 659 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: B 797 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7722 (mmpt) REVERT: B 844 LYS cc_start: 0.5934 (mmtt) cc_final: 0.5287 (mttp) REVERT: B 857 ASN cc_start: 0.8692 (p0) cc_final: 0.8460 (p0) REVERT: B 991 ASP cc_start: 0.7620 (p0) cc_final: 0.7005 (p0) REVERT: B 1005 MET cc_start: 0.9095 (mtt) cc_final: 0.8806 (mtt) REVERT: B 1114 TYR cc_start: 0.8533 (t80) cc_final: 0.8256 (t80) REVERT: C 134 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: C 135 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7086 (mm) REVERT: C 151 HIS cc_start: 0.6751 (OUTLIER) cc_final: 0.6466 (m90) REVERT: C 161 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7040 (pp20) REVERT: C 274 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7185 (ttt-90) REVERT: C 339 GLU cc_start: 0.7460 (tp30) cc_final: 0.7182 (tp30) REVERT: E 85 LYS cc_start: 0.7829 (mtpt) cc_final: 0.6975 (pmmt) REVERT: E 88 LYS cc_start: 0.7356 (mmmt) cc_final: 0.7092 (mtpp) REVERT: E 116 GLN cc_start: 0.7259 (tp40) cc_final: 0.6836 (tm130) REVERT: E 120 ASP cc_start: 0.7569 (m-30) cc_final: 0.6975 (m-30) REVERT: H 37 MET cc_start: 0.7807 (mtp) cc_final: 0.7595 (mtm) REVERT: H 80 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6807 (t70) REVERT: K 79 LYS cc_start: 0.8433 (ptpt) cc_final: 0.8145 (ptpp) REVERT: K 98 ARG cc_start: 0.8155 (ttp-170) cc_final: 0.7949 (ttp-170) REVERT: K 119 LYS cc_start: 0.8046 (tmtt) cc_final: 0.7783 (tmtm) REVERT: G 105 ILE cc_start: -0.0905 (mt) cc_final: -0.1171 (mt) outliers start: 204 outliers final: 67 residues processed: 843 average time/residue: 0.7163 time to fit residues: 723.0822 Evaluate side-chains 587 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 494 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 TRP Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 206 PRO Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 1045 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1184 LYS Chi-restraints excluded: chain A residue 1186 GLU Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1340 ARG Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 429 PRO Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 797 LYS Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 866 CYS Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.0370 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN A 347 GLN A 395 GLN ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN A 486 ASN A 499 ASN A 551 ASN A 557 HIS A 564 HIS A 595 ASN A 597 HIS A 600 GLN A 617 GLN A 632 GLN A 652 HIS A 700 HIS A 728 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN A 847 GLN A 850 HIS A 859 ASN A 888 GLN A 918 GLN A1051 GLN A1067 HIS A1068 HIS A1076 GLN A1097 GLN A1109 ASN A1118 GLN A1136 GLN A1177 GLN A1300 GLN A1329 GLN A1579 ASN A1717 GLN B 18 HIS B 97 ASN B 150 ASN B 219 HIS B 280 ASN B 313 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN B 461 ASN B 473 HIS B 501 HIS B 523 GLN B 580 HIS B 709 ASN B 734 ASN B 846 ASN ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 59 ASN C 127 GLN C 143 GLN ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 290 ASN E 43 GLN E 116 GLN E 133 GLN E 210 GLN H 76 ASN I 8 ASN I 33 GLN K 81 ASN K 85 GLN N 88 GLN M 34 GLN M 72 ASN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.177114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.137708 restraints weight = 36558.773| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.81 r_work: 0.3407 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 33872 Z= 0.170 Angle : 0.750 13.358 45959 Z= 0.395 Chirality : 0.049 0.324 5093 Planarity : 0.006 0.072 5797 Dihedral : 13.442 179.037 5144 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.12 % Favored : 92.78 % Rotamer: Outliers : 5.17 % Allowed : 15.07 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 4001 helix: -0.95 (0.14), residues: 1227 sheet: -1.46 (0.19), residues: 660 loop : -2.28 (0.12), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1036 TYR 0.022 0.002 TYR B 826 PHE 0.018 0.002 PHE B 265 TRP 0.021 0.002 TRP A 391 HIS 0.011 0.001 HIS A1509 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (33855) covalent geometry : angle 0.74394 / 0.39 (45947) hydrogen bonds : bond 0.05504 / 3.69 ( 1035) hydrogen bonds : angle 5.34002 / 3.77 ( 2849) metal coordination : bond 0.01189 / 0.54 ( 17) metal coordination : angle 5.77902 / 3.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 534 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7384 (mtmt) cc_final: 0.6997 (mmtt) REVERT: A 127 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7433 (mt) REVERT: A 200 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8803 (mmp) REVERT: A 204 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6320 (mpp80) REVERT: A 381 GLN cc_start: 0.4631 (OUTLIER) cc_final: 0.3930 (tt0) REVERT: A 408 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6664 (pmtt) REVERT: A 411 MET cc_start: 0.7582 (mpp) cc_final: 0.7368 (mpt) REVERT: A 465 LYS cc_start: 0.8756 (tttm) cc_final: 0.8511 (tttp) REVERT: A 535 THR cc_start: 0.7886 (OUTLIER) cc_final: 0.7679 (m) REVERT: A 550 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8066 (mp) REVERT: A 567 ARG cc_start: 0.7962 (tpt90) cc_final: 0.7283 (tpt-90) REVERT: A 635 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.7543 (mpp) REVERT: A 708 LYS cc_start: 0.8860 (mtpp) cc_final: 0.8575 (mtpp) REVERT: A 973 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: A 1051 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6801 (pt0) REVERT: A 1174 TRP cc_start: 0.7445 (t-100) cc_final: 0.7189 (t60) REVERT: A 1180 LYS cc_start: 0.5426 (mmtt) cc_final: 0.5050 (pttp) REVERT: A 1191 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7663 (ttp-110) REVERT: A 1239 MET cc_start: 0.3307 (ptt) cc_final: 0.2677 (mtp) REVERT: A 1263 MET cc_start: 0.8048 (ppp) cc_final: 0.7837 (pp-130) REVERT: A 1340 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.6179 (ttp80) REVERT: A 1619 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7484 (mmt-90) REVERT: A 1677 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8101 (m) REVERT: B 8 ARG cc_start: 0.7187 (mtt180) cc_final: 0.6304 (mmp-170) REVERT: B 20 THR cc_start: 0.7668 (p) cc_final: 0.7451 (p) REVERT: B 32 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7813 (tmtt) REVERT: B 59 GLN cc_start: 0.7804 (mm110) cc_final: 0.7243 (mt0) REVERT: B 111 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8254 (ptm160) REVERT: B 131 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7667 (ttmt) REVERT: B 272 LYS cc_start: 0.7747 (mtmt) cc_final: 0.7114 (mtmm) REVERT: B 283 SER cc_start: 0.8542 (t) cc_final: 0.8332 (m) REVERT: B 325 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7217 (tp30) REVERT: B 345 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7077 (tpp) REVERT: B 430 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8673 (t80) REVERT: B 481 MET cc_start: 0.7959 (mtt) cc_final: 0.7628 (mtm) REVERT: B 542 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7524 (tt) REVERT: B 659 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: B 797 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7477 (mmpt) REVERT: B 1018 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7030 (mtp180) REVERT: B 1040 MET cc_start: 0.9011 (mtp) cc_final: 0.8688 (mtp) REVERT: B 1114 TYR cc_start: 0.8949 (t80) cc_final: 0.8669 (t80) REVERT: C 166 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7735 (p90) REVERT: E 79 GLU cc_start: 0.7632 (mp0) cc_final: 0.7141 (mp0) REVERT: E 95 GLN cc_start: 0.7239 (pt0) cc_final: 0.7014 (pt0) REVERT: E 116 GLN cc_start: 0.7623 (tp-100) cc_final: 0.7052 (tm130) REVERT: E 143 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7592 (pt0) REVERT: H 37 MET cc_start: 0.8015 (mtp) cc_final: 0.7796 (mtm) REVERT: H 80 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6797 (t70) REVERT: K 79 LYS cc_start: 0.8694 (ptpt) cc_final: 0.8383 (pttp) REVERT: N 83 LEU cc_start: 0.6856 (mt) cc_final: 0.6645 (mm) REVERT: N 116 ARG cc_start: 0.4686 (OUTLIER) cc_final: 0.3324 (tpt170) REVERT: G 104 ASP cc_start: -0.0114 (p0) cc_final: -0.0328 (p0) REVERT: M 33 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6409 (pp) outliers start: 183 outliers final: 65 residues processed: 663 average time/residue: 0.7147 time to fit residues: 568.9471 Evaluate side-chains 549 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 456 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 TRP Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1340 ARG Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 797 LYS Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 866 CYS Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1104 SER Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain K residue 61 LYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain M residue 33 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 204 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 280 optimal weight: 0.4980 chunk 303 optimal weight: 0.0020 chunk 253 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 191 optimal weight: 0.0970 chunk 5 optimal weight: 6.9990 chunk 373 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 333 optimal weight: 10.0000 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS A 564 HIS A 578 HIS ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1033 GLN A1097 GLN A1610 ASN B 313 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN B 449 GLN B 580 HIS B 639 GLN B 680 ASN B 887 HIS ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN C 166 HIS E 133 GLN E 210 GLN H 76 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.179362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140468 restraints weight = 36628.366| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.82 r_work: 0.3444 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33872 Z= 0.132 Angle : 0.660 12.125 45959 Z= 0.347 Chirality : 0.046 0.335 5093 Planarity : 0.005 0.062 5797 Dihedral : 12.610 169.993 5055 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.07 % Favored : 92.90 % Rotamer: Outliers : 5.00 % Allowed : 16.85 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.02 (0.13), residues: 4001 helix: -0.28 (0.15), residues: 1215 sheet: -1.29 (0.19), residues: 638 loop : -2.03 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1694 TYR 0.021 0.002 TYR A 754 PHE 0.020 0.001 PHE M 41 TRP 0.028 0.001 TRP B 120 HIS 0.007 0.001 HIS A1509 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (33855) covalent geometry : angle 0.65494 / 0.35 (45947) hydrogen bonds : bond 0.04603 / 3.09 ( 1035) hydrogen bonds : angle 4.94031 / 3.50 ( 2849) metal coordination : bond 0.00627 / 0.35 ( 17) metal coordination : angle 4.95348 / 2.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 502 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7483 (mtmt) cc_final: 0.6931 (mmtt) REVERT: A 172 ASN cc_start: 0.7666 (t0) cc_final: 0.7199 (t0) REVERT: A 200 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8674 (mmp) REVERT: A 204 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6353 (mpp80) REVERT: A 381 GLN cc_start: 0.4544 (OUTLIER) cc_final: 0.4100 (tt0) REVERT: A 423 LYS cc_start: 0.7603 (mmtt) cc_final: 0.7388 (mmmt) REVERT: A 465 LYS cc_start: 0.8743 (tttm) cc_final: 0.8541 (tttp) REVERT: A 478 GLN cc_start: 0.7459 (tt0) cc_final: 0.6626 (mp10) REVERT: A 500 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7661 (mt-10) REVERT: A 567 ARG cc_start: 0.7971 (tpt90) cc_final: 0.7297 (tpt-90) REVERT: A 708 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8498 (mptt) REVERT: A 973 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: A 1122 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7639 (ttp80) REVERT: A 1174 TRP cc_start: 0.7397 (t-100) cc_final: 0.7137 (t60) REVERT: A 1180 LYS cc_start: 0.5216 (mmtt) cc_final: 0.4870 (pttp) REVERT: A 1191 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7687 (ttp-110) REVERT: A 1239 MET cc_start: 0.3420 (ptt) cc_final: 0.2799 (mtp) REVERT: A 1243 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8361 (mt) REVERT: A 1263 MET cc_start: 0.7845 (ppp) cc_final: 0.7622 (pp-130) REVERT: A 1316 GLN cc_start: 0.5017 (OUTLIER) cc_final: 0.4497 (pp30) REVERT: A 1340 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.6132 (ttp80) REVERT: A 1637 ASP cc_start: 0.8311 (t0) cc_final: 0.8045 (t0) REVERT: B 8 ARG cc_start: 0.7214 (mtt180) cc_final: 0.6386 (mmp-170) REVERT: B 20 THR cc_start: 0.7613 (p) cc_final: 0.7369 (p) REVERT: B 32 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7650 (tmtt) REVERT: B 59 GLN cc_start: 0.7744 (mm110) cc_final: 0.7257 (mt0) REVERT: B 111 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8171 (ptm-80) REVERT: B 120 TRP cc_start: 0.6480 (p-90) cc_final: 0.6134 (p-90) REVERT: B 131 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7658 (ttmt) REVERT: B 144 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7914 (ptmt) REVERT: B 193 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7949 (ttm) REVERT: B 197 LYS cc_start: 0.8334 (tttt) cc_final: 0.8071 (tppt) REVERT: B 272 LYS cc_start: 0.7697 (mtmt) cc_final: 0.7066 (mtmm) REVERT: B 283 SER cc_start: 0.8596 (t) cc_final: 0.8351 (m) REVERT: B 325 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7196 (tp30) REVERT: B 337 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7052 (mttp) REVERT: B 481 MET cc_start: 0.7954 (mtt) cc_final: 0.7651 (mtm) REVERT: B 542 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7324 (tt) REVERT: B 659 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: B 797 LYS cc_start: 0.8093 (ttpt) cc_final: 0.7478 (mmtt) REVERT: B 842 LYS cc_start: 0.7657 (ptpt) cc_final: 0.7257 (mmtm) REVERT: B 857 ASN cc_start: 0.9006 (p0) cc_final: 0.8706 (p0) REVERT: B 1018 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.6957 (mtp180) REVERT: B 1040 MET cc_start: 0.9064 (mtp) cc_final: 0.8802 (mtp) REVERT: C 123 GLU cc_start: 0.8418 (pt0) cc_final: 0.8207 (pt0) REVERT: C 295 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.7782 (mmtt) REVERT: C 298 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8216 (tmm160) REVERT: E 79 GLU cc_start: 0.7541 (mp0) cc_final: 0.7087 (mp0) REVERT: E 95 GLN cc_start: 0.7025 (pt0) cc_final: 0.6696 (pp30) REVERT: E 116 GLN cc_start: 0.7735 (tp-100) cc_final: 0.6968 (tm-30) REVERT: E 128 GLU cc_start: 0.7719 (pt0) cc_final: 0.7446 (pt0) REVERT: E 143 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: F 95 LYS cc_start: 0.7312 (tttp) cc_final: 0.6880 (mtmm) REVERT: F 100 ARG cc_start: 0.7642 (mtt-85) cc_final: 0.7329 (mtp-110) REVERT: H 31 GLU cc_start: 0.7793 (tt0) cc_final: 0.7562 (tp30) REVERT: H 37 MET cc_start: 0.7891 (mtp) cc_final: 0.7614 (mtm) REVERT: H 74 GLU cc_start: 0.7556 (tt0) cc_final: 0.7274 (tt0) REVERT: K 79 LYS cc_start: 0.8685 (ptpt) cc_final: 0.8341 (pttp) REVERT: N 116 ARG cc_start: 0.4670 (OUTLIER) cc_final: 0.3836 (ttt90) REVERT: G 116 ILE cc_start: 0.1041 (tp) cc_final: 0.0808 (tt) outliers start: 177 outliers final: 60 residues processed: 618 average time/residue: 0.7366 time to fit residues: 542.3939 Evaluate side-chains 527 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 447 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1340 ARG Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 866 CYS Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 330 optimal weight: 7.9990 chunk 324 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 271 optimal weight: 0.1980 chunk 338 optimal weight: 0.0980 chunk 370 optimal weight: 8.9990 chunk 273 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 345 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 ASN ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS A 564 HIS A 753 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN A1097 GLN A1295 GLN B 147 ASN B 223 ASN B 237 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS B 580 HIS ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 945 HIS C 42 GLN C 143 GLN E 133 GLN E 210 GLN H 44 ASN M 87 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.175636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137382 restraints weight = 36668.197| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.80 r_work: 0.3395 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33872 Z= 0.174 Angle : 0.674 10.450 45959 Z= 0.352 Chirality : 0.047 0.288 5093 Planarity : 0.005 0.067 5797 Dihedral : 12.306 170.171 5020 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.20 % Favored : 92.78 % Rotamer: Outliers : 5.02 % Allowed : 18.09 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.85 (0.13), residues: 4001 helix: -0.18 (0.15), residues: 1234 sheet: -1.24 (0.19), residues: 649 loop : -1.89 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1694 TYR 0.024 0.002 TYR A 579 PHE 0.018 0.002 PHE C 336 TRP 0.020 0.002 TRP B 120 HIS 0.008 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (33855) covalent geometry : angle 0.67042 / 0.35 (45947) hydrogen bonds : bond 0.04771 / 3.18 ( 1035) hydrogen bonds : angle 4.83242 / 3.42 ( 2849) metal coordination : bond 0.00378 / 0.23 ( 17) metal coordination : angle 4.62479 / 2.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 483 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7583 (mtmt) cc_final: 0.6945 (mmtt) REVERT: A 127 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7359 (mt) REVERT: A 139 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: A 200 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8665 (mmp) REVERT: A 204 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6392 (mpp80) REVERT: A 381 GLN cc_start: 0.4545 (OUTLIER) cc_final: 0.4160 (tt0) REVERT: A 423 LYS cc_start: 0.7619 (mmtt) cc_final: 0.7384 (mmmt) REVERT: A 478 GLN cc_start: 0.7463 (tt0) cc_final: 0.6601 (mp10) REVERT: A 512 MET cc_start: 0.7196 (tpp) cc_final: 0.6902 (tpp) REVERT: A 567 ARG cc_start: 0.8159 (tpt90) cc_final: 0.7439 (tpp80) REVERT: A 635 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.7271 (mpp) REVERT: A 708 LYS cc_start: 0.8860 (mtpp) cc_final: 0.8546 (mptt) REVERT: A 891 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: A 973 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7730 (pt0) REVERT: A 1174 TRP cc_start: 0.7411 (t-100) cc_final: 0.7139 (t60) REVERT: A 1180 LYS cc_start: 0.5203 (mmtt) cc_final: 0.4873 (pttp) REVERT: A 1191 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7710 (ttp-110) REVERT: A 1239 MET cc_start: 0.3577 (ptt) cc_final: 0.2789 (mtp) REVERT: A 1243 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8394 (mt) REVERT: A 1263 MET cc_start: 0.7861 (ppp) cc_final: 0.7632 (pp-130) REVERT: A 1269 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7248 (tp) REVERT: A 1316 GLN cc_start: 0.4979 (OUTLIER) cc_final: 0.4604 (pp30) REVERT: A 1340 ARG cc_start: 0.6226 (OUTLIER) cc_final: 0.5952 (ttp80) REVERT: A 1523 LEU cc_start: 0.4375 (OUTLIER) cc_final: 0.4027 (pp) REVERT: A 1637 ASP cc_start: 0.8421 (t0) cc_final: 0.8107 (t70) REVERT: B 8 ARG cc_start: 0.7273 (mtt180) cc_final: 0.6376 (mmp-170) REVERT: B 20 THR cc_start: 0.7782 (p) cc_final: 0.7566 (p) REVERT: B 32 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7628 (tmtt) REVERT: B 59 GLN cc_start: 0.7776 (mm110) cc_final: 0.7328 (mt0) REVERT: B 94 LYS cc_start: 0.8166 (tptt) cc_final: 0.7859 (tptp) REVERT: B 120 TRP cc_start: 0.6549 (p-90) cc_final: 0.5722 (p-90) REVERT: B 131 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7659 (ttmt) REVERT: B 144 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8060 (ptmt) REVERT: B 261 ASP cc_start: 0.8117 (m-30) cc_final: 0.7844 (m-30) REVERT: B 272 LYS cc_start: 0.7682 (mtmt) cc_final: 0.7024 (mtmm) REVERT: B 325 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7218 (tp30) REVERT: B 337 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6938 (mttp) REVERT: B 481 MET cc_start: 0.8002 (mtt) cc_final: 0.7683 (mtm) REVERT: B 659 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: B 797 LYS cc_start: 0.8129 (ttpt) cc_final: 0.7503 (mmtt) REVERT: B 857 ASN cc_start: 0.9067 (p0) cc_final: 0.8726 (p0) REVERT: B 1018 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.6878 (mtp180) REVERT: B 1040 MET cc_start: 0.9073 (mtp) cc_final: 0.8835 (mtp) REVERT: C 295 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.7736 (mmtt) REVERT: C 298 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8216 (tmm160) REVERT: E 79 GLU cc_start: 0.7585 (mp0) cc_final: 0.7109 (mp0) REVERT: E 95 GLN cc_start: 0.7006 (pt0) cc_final: 0.6675 (pp30) REVERT: E 128 GLU cc_start: 0.7813 (pt0) cc_final: 0.7539 (pt0) REVERT: E 143 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: F 100 ARG cc_start: 0.7677 (mtt-85) cc_final: 0.7335 (mtp-110) REVERT: H 37 MET cc_start: 0.7991 (mtp) cc_final: 0.7747 (mtm) REVERT: I 17 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.5999 (mt) REVERT: J 58 LYS cc_start: 0.8816 (mttp) cc_final: 0.8613 (mtmt) REVERT: K 29 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8267 (mpp) REVERT: K 79 LYS cc_start: 0.8734 (ptpt) cc_final: 0.8382 (pttp) REVERT: N 83 LEU cc_start: 0.6871 (mt) cc_final: 0.6628 (mm) REVERT: N 94 LEU cc_start: 0.5306 (pp) cc_final: 0.5089 (pt) REVERT: N 116 ARG cc_start: 0.4576 (OUTLIER) cc_final: 0.3726 (ttt90) outliers start: 178 outliers final: 72 residues processed: 595 average time/residue: 0.7285 time to fit residues: 516.3045 Evaluate side-chains 538 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 441 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1340 ARG Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 105 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 9 optimal weight: 6.9990 chunk 266 optimal weight: 3.9990 chunk 311 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 399 optimal weight: 50.0000 chunk 155 optimal weight: 0.7980 chunk 301 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 ASN ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN A1097 GLN ** A1324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 335 HIS B 580 HIS ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN E 210 GLN H 44 ASN H 76 ASN M 87 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.174888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136319 restraints weight = 36689.056| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.79 r_work: 0.3383 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33872 Z= 0.176 Angle : 0.671 12.040 45959 Z= 0.348 Chirality : 0.047 0.257 5093 Planarity : 0.005 0.065 5797 Dihedral : 12.135 171.379 5014 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.40 % Favored : 92.58 % Rotamer: Outliers : 5.45 % Allowed : 19.28 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.75 (0.13), residues: 4001 helix: -0.07 (0.15), residues: 1233 sheet: -1.22 (0.19), residues: 667 loop : -1.82 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1122 TYR 0.022 0.002 TYR A 164 PHE 0.018 0.002 PHE C 336 TRP 0.018 0.002 TRP C 40 HIS 0.007 0.001 HIS A 995 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (33855) covalent geometry : angle 0.66677 / 0.35 (45947) hydrogen bonds : bond 0.04688 / 3.13 ( 1035) hydrogen bonds : angle 4.77583 / 3.37 ( 2849) metal coordination : bond 0.00433 / 0.27 ( 17) metal coordination : angle 4.89677 / 2.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 475 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7551 (mtmt) cc_final: 0.6847 (mmtt) REVERT: A 127 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7318 (mt) REVERT: A 170 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6125 (mp10) REVERT: A 200 MET cc_start: 0.8999 (tpt) cc_final: 0.8718 (mmp) REVERT: A 204 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6321 (mpp80) REVERT: A 381 GLN cc_start: 0.4463 (OUTLIER) cc_final: 0.4139 (tt0) REVERT: A 423 LYS cc_start: 0.7589 (mmtt) cc_final: 0.7346 (mmmt) REVERT: A 478 GLN cc_start: 0.7483 (tt0) cc_final: 0.6616 (mp10) REVERT: A 567 ARG cc_start: 0.8158 (tpt90) cc_final: 0.7448 (tpp80) REVERT: A 603 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8417 (tt) REVERT: A 635 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.7185 (mpp) REVERT: A 708 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8559 (mtpp) REVERT: A 891 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: A 973 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: A 1119 GLU cc_start: 0.7821 (tp30) cc_final: 0.7446 (tp30) REVERT: A 1122 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7740 (ttp80) REVERT: A 1174 TRP cc_start: 0.7397 (t-100) cc_final: 0.7091 (t60) REVERT: A 1180 LYS cc_start: 0.5304 (mmtt) cc_final: 0.4872 (pttp) REVERT: A 1191 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7709 (ttp-110) REVERT: A 1239 MET cc_start: 0.3653 (ptt) cc_final: 0.2833 (mtp) REVERT: A 1243 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8358 (mt) REVERT: A 1263 MET cc_start: 0.7884 (ppp) cc_final: 0.7657 (pp-130) REVERT: A 1269 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7244 (tp) REVERT: A 1316 GLN cc_start: 0.5140 (OUTLIER) cc_final: 0.4731 (pp30) REVERT: A 1340 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5896 (ttp80) REVERT: A 1523 LEU cc_start: 0.4346 (OUTLIER) cc_final: 0.4001 (pp) REVERT: A 1581 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6866 (tp30) REVERT: A 1624 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: A 1637 ASP cc_start: 0.8334 (t0) cc_final: 0.8061 (t0) REVERT: B 8 ARG cc_start: 0.7304 (mtt180) cc_final: 0.6432 (mmp-170) REVERT: B 20 THR cc_start: 0.7736 (p) cc_final: 0.7504 (p) REVERT: B 32 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7337 (tmtt) REVERT: B 59 GLN cc_start: 0.7723 (mm110) cc_final: 0.7340 (mt0) REVERT: B 120 TRP cc_start: 0.6539 (p-90) cc_final: 0.6192 (p-90) REVERT: B 197 LYS cc_start: 0.8360 (tttt) cc_final: 0.8057 (tppt) REVERT: B 272 LYS cc_start: 0.7600 (mtmt) cc_final: 0.6940 (mttp) REVERT: B 325 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7118 (tp30) REVERT: B 436 THR cc_start: 0.8938 (m) cc_final: 0.8721 (p) REVERT: B 481 MET cc_start: 0.7970 (mtt) cc_final: 0.7658 (mtm) REVERT: B 562 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8130 (tmm) REVERT: B 659 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: B 694 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: B 797 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7472 (mmpt) REVERT: B 842 LYS cc_start: 0.7985 (ptpt) cc_final: 0.7339 (mmtm) REVERT: B 1018 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.6847 (mtp180) REVERT: B 1068 HIS cc_start: 0.7660 (OUTLIER) cc_final: 0.6577 (p90) REVERT: C 295 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.7806 (mmtt) REVERT: C 298 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8178 (tmm160) REVERT: E 85 LYS cc_start: 0.7891 (mtpt) cc_final: 0.6923 (pmmt) REVERT: E 95 GLN cc_start: 0.6869 (pt0) cc_final: 0.6545 (pp30) REVERT: E 128 GLU cc_start: 0.7845 (pt0) cc_final: 0.7573 (pt0) REVERT: E 143 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: E 174 GLN cc_start: 0.8615 (mm110) cc_final: 0.8359 (mm110) REVERT: F 100 ARG cc_start: 0.7622 (mtt-85) cc_final: 0.7309 (mtp-110) REVERT: H 37 MET cc_start: 0.7989 (mtp) cc_final: 0.7765 (mtm) REVERT: I 17 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6165 (mt) REVERT: K 79 LYS cc_start: 0.8741 (ptpt) cc_final: 0.8370 (pttp) REVERT: N 83 LEU cc_start: 0.7032 (mt) cc_final: 0.6717 (mm) REVERT: N 94 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.5243 (pt) REVERT: N 116 ARG cc_start: 0.4738 (OUTLIER) cc_final: 0.3957 (ttt90) outliers start: 193 outliers final: 82 residues processed: 603 average time/residue: 0.7214 time to fit residues: 520.1970 Evaluate side-chains 560 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 450 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1186 GLU Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1340 ARG Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1692 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 694 GLN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1068 HIS Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 116 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 284 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 299 optimal weight: 5.9990 chunk 344 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 353 optimal weight: 0.5980 chunk 361 optimal weight: 10.0000 chunk 378 optimal weight: 0.0170 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN A1097 GLN A1118 GLN B 223 ASN B 536 ASN B 580 HIS ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1060 ASN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN H 44 ASN H 76 ASN M 87 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.177777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.138737 restraints weight = 36549.402| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.78 r_work: 0.3420 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33872 Z= 0.124 Angle : 0.621 10.757 45959 Z= 0.322 Chirality : 0.044 0.200 5093 Planarity : 0.005 0.061 5797 Dihedral : 11.941 172.518 4999 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.87 % Favored : 93.10 % Rotamer: Outliers : 4.43 % Allowed : 20.91 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.53 (0.13), residues: 4001 helix: 0.16 (0.15), residues: 1226 sheet: -1.07 (0.20), residues: 643 loop : -1.72 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1694 TYR 0.029 0.001 TYR A1092 PHE 0.017 0.001 PHE C 336 TRP 0.018 0.001 TRP A 9 HIS 0.004 0.001 HIS A 995 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (33855) covalent geometry : angle 0.61670 / 0.32 (45947) hydrogen bonds : bond 0.04114 / 2.76 ( 1035) hydrogen bonds : angle 4.63612 / 3.29 ( 2849) metal coordination : bond 0.00326 / 0.20 ( 17) metal coordination : angle 4.51827 / 2.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 476 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7546 (mtmt) cc_final: 0.6868 (mmtt) REVERT: A 127 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7079 (mt) REVERT: A 170 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6027 (mp10) REVERT: A 200 MET cc_start: 0.8930 (tpt) cc_final: 0.8588 (mmp) REVERT: A 204 ARG cc_start: 0.6816 (mpp-170) cc_final: 0.6298 (mpp80) REVERT: A 381 GLN cc_start: 0.4508 (OUTLIER) cc_final: 0.4255 (tt0) REVERT: A 410 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.6122 (mtm) REVERT: A 478 GLN cc_start: 0.7460 (tt0) cc_final: 0.6630 (mp10) REVERT: A 521 GLN cc_start: 0.6620 (mp10) cc_final: 0.6227 (mm-40) REVERT: A 567 ARG cc_start: 0.8093 (tpt90) cc_final: 0.7395 (tpp80) REVERT: A 635 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.7218 (mpp) REVERT: A 708 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8512 (mptt) REVERT: A 875 GLU cc_start: 0.7637 (tp30) cc_final: 0.7339 (tp30) REVERT: A 973 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7647 (pt0) REVERT: A 993 ILE cc_start: 0.8901 (mt) cc_final: 0.8687 (mm) REVERT: A 1174 TRP cc_start: 0.7293 (t-100) cc_final: 0.7047 (t60) REVERT: A 1180 LYS cc_start: 0.5288 (mmtt) cc_final: 0.4862 (pttp) REVERT: A 1191 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7619 (ttp-110) REVERT: A 1239 MET cc_start: 0.3642 (ptt) cc_final: 0.2822 (mtp) REVERT: A 1243 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8366 (mt) REVERT: A 1263 MET cc_start: 0.7794 (ppp) cc_final: 0.7570 (pp-130) REVERT: A 1316 GLN cc_start: 0.5222 (OUTLIER) cc_final: 0.4806 (pp30) REVERT: A 1540 MET cc_start: 0.3104 (OUTLIER) cc_final: 0.2853 (mtt) REVERT: A 1581 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6854 (tp30) REVERT: A 1624 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: A 1637 ASP cc_start: 0.8350 (t0) cc_final: 0.8112 (t0) REVERT: B 8 ARG cc_start: 0.7288 (mtt180) cc_final: 0.6390 (mmp-170) REVERT: B 20 THR cc_start: 0.7637 (p) cc_final: 0.7403 (p) REVERT: B 59 GLN cc_start: 0.7616 (mm110) cc_final: 0.7302 (mt0) REVERT: B 120 TRP cc_start: 0.6540 (p-90) cc_final: 0.6212 (p-90) REVERT: B 197 LYS cc_start: 0.8367 (tttt) cc_final: 0.8029 (tppt) REVERT: B 272 LYS cc_start: 0.7493 (mtmt) cc_final: 0.6819 (mtmm) REVERT: B 325 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7152 (tp30) REVERT: B 337 LYS cc_start: 0.7333 (mppt) cc_final: 0.6972 (mttm) REVERT: B 436 THR cc_start: 0.8901 (m) cc_final: 0.8673 (p) REVERT: B 481 MET cc_start: 0.7991 (mtt) cc_final: 0.7701 (mtm) REVERT: B 542 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.6656 (tt) REVERT: B 548 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7565 (mmm160) REVERT: B 550 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.7582 (m-10) REVERT: B 562 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7928 (tmm) REVERT: B 593 MET cc_start: 0.8511 (ttp) cc_final: 0.8272 (ttm) REVERT: B 659 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: B 797 LYS cc_start: 0.8022 (ttpt) cc_final: 0.7396 (mmtt) REVERT: B 842 LYS cc_start: 0.8010 (ptpt) cc_final: 0.7532 (mmtt) REVERT: B 857 ASN cc_start: 0.8991 (p0) cc_final: 0.8671 (p0) REVERT: B 1018 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.6714 (mtp180) REVERT: B 1068 HIS cc_start: 0.7610 (OUTLIER) cc_final: 0.6484 (p90) REVERT: C 243 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6863 (pm20) REVERT: C 298 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8132 (tmm160) REVERT: E 116 GLN cc_start: 0.7715 (tp-100) cc_final: 0.7391 (tp40) REVERT: E 143 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: H 37 MET cc_start: 0.7897 (mtp) cc_final: 0.7654 (mtm) REVERT: I 29 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5790 (tp) REVERT: K 60 MET cc_start: 0.8489 (mmp) cc_final: 0.8219 (mtp) REVERT: K 79 LYS cc_start: 0.8748 (ptpt) cc_final: 0.8185 (pttp) REVERT: N 83 LEU cc_start: 0.6993 (mt) cc_final: 0.6661 (mm) REVERT: N 94 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.5119 (pt) REVERT: N 116 ARG cc_start: 0.4341 (OUTLIER) cc_final: 0.3659 (ttt90) REVERT: M 39 MET cc_start: 0.4258 (OUTLIER) cc_final: 0.4000 (ppp) outliers start: 157 outliers final: 63 residues processed: 585 average time/residue: 0.7326 time to fit residues: 510.8593 Evaluate side-chains 535 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 446 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1540 MET Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1068 HIS Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain M residue 39 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 19 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 338 optimal weight: 3.9990 chunk 332 optimal weight: 7.9990 chunk 390 optimal weight: 0.3980 chunk 364 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 393 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN ** A1324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS B 941 HIS B1060 ASN E 210 GLN H 44 ASN K 85 GLN M 87 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.173327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133272 restraints weight = 36722.204| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.84 r_work: 0.3316 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 33872 Z= 0.254 Angle : 0.733 12.331 45959 Z= 0.378 Chirality : 0.050 0.232 5093 Planarity : 0.005 0.064 5797 Dihedral : 12.000 173.631 4984 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.15 % Favored : 91.83 % Rotamer: Outliers : 5.08 % Allowed : 20.80 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.72 (0.13), residues: 4001 helix: -0.11 (0.15), residues: 1244 sheet: -1.17 (0.19), residues: 674 loop : -1.78 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1694 TYR 0.024 0.002 TYR E 90 PHE 0.020 0.002 PHE B 265 TRP 0.016 0.002 TRP B 565 HIS 0.008 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.25 (33855) covalent geometry : angle 0.72931 / 0.38 (45947) hydrogen bonds : bond 0.05196 / 3.44 ( 1035) hydrogen bonds : angle 4.81007 / 3.38 ( 2849) metal coordination : bond 0.00513 / 0.30 ( 17) metal coordination : angle 4.78368 / 2.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 453 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7538 (mtmt) cc_final: 0.6853 (mmtt) REVERT: A 127 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7148 (mt) REVERT: A 170 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.5961 (mp10) REVERT: A 200 MET cc_start: 0.8990 (tpt) cc_final: 0.8627 (mmp) REVERT: A 204 ARG cc_start: 0.6800 (mpp-170) cc_final: 0.6245 (mpp80) REVERT: A 381 GLN cc_start: 0.4516 (OUTLIER) cc_final: 0.4192 (tt0) REVERT: A 423 LYS cc_start: 0.7637 (mmmt) cc_final: 0.7357 (mmmm) REVERT: A 478 GLN cc_start: 0.7317 (tt0) cc_final: 0.6364 (mp10) REVERT: A 567 ARG cc_start: 0.8178 (tpt90) cc_final: 0.7234 (tpp80) REVERT: A 603 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7965 (tt) REVERT: A 635 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.7150 (mpp) REVERT: A 875 GLU cc_start: 0.7503 (tp30) cc_final: 0.7223 (tp30) REVERT: A 973 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: A 1122 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7714 (ttp80) REVERT: A 1174 TRP cc_start: 0.7107 (t-100) cc_final: 0.6791 (t60) REVERT: A 1180 LYS cc_start: 0.5405 (mmtt) cc_final: 0.4828 (pttp) REVERT: A 1191 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7487 (ttp-110) REVERT: A 1239 MET cc_start: 0.3529 (ptt) cc_final: 0.2670 (mtp) REVERT: A 1243 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8214 (mt) REVERT: A 1263 MET cc_start: 0.7783 (ppp) cc_final: 0.7443 (pp-130) REVERT: A 1316 GLN cc_start: 0.4889 (OUTLIER) cc_final: 0.4474 (pp30) REVERT: A 1540 MET cc_start: 0.2833 (OUTLIER) cc_final: 0.2615 (mtt) REVERT: A 1624 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: A 1637 ASP cc_start: 0.8519 (t0) cc_final: 0.8275 (t70) REVERT: B 8 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6108 (mmp-170) REVERT: B 20 THR cc_start: 0.7777 (p) cc_final: 0.7555 (p) REVERT: B 32 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7346 (tmtt) REVERT: B 59 GLN cc_start: 0.7437 (mm110) cc_final: 0.7052 (mt0) REVERT: B 94 LYS cc_start: 0.8277 (tptt) cc_final: 0.7875 (tptp) REVERT: B 120 TRP cc_start: 0.6418 (p-90) cc_final: 0.6041 (p-90) REVERT: B 197 LYS cc_start: 0.8290 (tttt) cc_final: 0.7827 (tppt) REVERT: B 272 LYS cc_start: 0.7443 (mtmt) cc_final: 0.6577 (mtmt) REVERT: B 325 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6948 (tp30) REVERT: B 436 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8546 (p) REVERT: B 481 MET cc_start: 0.7784 (mtt) cc_final: 0.7386 (mtm) REVERT: B 548 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7599 (mmm160) REVERT: B 550 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7925 (m-10) REVERT: B 562 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8172 (tmm) REVERT: B 659 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: B 694 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8008 (mt0) REVERT: B 842 LYS cc_start: 0.8154 (ptpt) cc_final: 0.7497 (mmtt) REVERT: B 1018 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.6541 (mtp180) REVERT: B 1068 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.6386 (p90) REVERT: B 1111 SER cc_start: 0.9126 (OUTLIER) cc_final: 0.8832 (m) REVERT: E 85 LYS cc_start: 0.7827 (mtpt) cc_final: 0.6808 (pmmt) REVERT: E 116 GLN cc_start: 0.7653 (tp-100) cc_final: 0.7346 (tp40) REVERT: E 143 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7822 (pt0) REVERT: F 95 LYS cc_start: 0.6633 (tttp) cc_final: 0.6204 (ttmt) REVERT: H 37 MET cc_start: 0.8032 (mtp) cc_final: 0.7811 (mtm) REVERT: H 98 ARG cc_start: 0.8589 (ttm170) cc_final: 0.8366 (ttp-110) REVERT: I 17 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6312 (mt) REVERT: I 29 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5870 (tp) REVERT: K 60 MET cc_start: 0.8699 (mmp) cc_final: 0.8383 (mtp) REVERT: K 79 LYS cc_start: 0.8524 (ptpt) cc_final: 0.8097 (pttp) REVERT: K 119 LYS cc_start: 0.7608 (tmtt) cc_final: 0.7347 (tmtm) REVERT: N 83 LEU cc_start: 0.6959 (mt) cc_final: 0.6581 (mm) REVERT: N 94 LEU cc_start: 0.5385 (OUTLIER) cc_final: 0.5092 (pt) REVERT: N 116 ARG cc_start: 0.4281 (OUTLIER) cc_final: 0.3443 (ttt90) outliers start: 180 outliers final: 87 residues processed: 574 average time/residue: 0.7644 time to fit residues: 521.4759 Evaluate side-chains 557 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 444 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1186 GLU Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1540 MET Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1646 ASP Chi-restraints excluded: chain A residue 1692 GLU Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 694 GLN Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1068 HIS Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 116 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 32 optimal weight: 0.9980 chunk 321 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 205 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 237 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 379 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A1097 GLN A1258 ASN B 580 HIS B1060 ASN E 210 GLN H 44 ASN H 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.175667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135665 restraints weight = 36690.312| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.83 r_work: 0.3378 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33872 Z= 0.126 Angle : 0.639 11.070 45959 Z= 0.331 Chirality : 0.045 0.239 5093 Planarity : 0.005 0.061 5797 Dihedral : 11.871 174.525 4982 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.07 % Favored : 92.90 % Rotamer: Outliers : 3.44 % Allowed : 22.61 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.47 (0.13), residues: 4001 helix: 0.17 (0.15), residues: 1239 sheet: -1.06 (0.20), residues: 657 loop : -1.67 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1694 TYR 0.027 0.001 TYR A 754 PHE 0.017 0.001 PHE I 19 TRP 0.018 0.001 TRP C 40 HIS 0.006 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (33855) covalent geometry : angle 0.63425 / 0.33 (45947) hydrogen bonds : bond 0.04237 / 2.84 ( 1035) hydrogen bonds : angle 4.66234 / 3.29 ( 2849) metal coordination : bond 0.00336 / 0.21 ( 17) metal coordination : angle 4.64822 / 2.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 461 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7534 (mtmt) cc_final: 0.6847 (mmtt) REVERT: A 127 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6832 (mt) REVERT: A 170 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.5935 (mp10) REVERT: A 200 MET cc_start: 0.8860 (tpt) cc_final: 0.8502 (mmp) REVERT: A 204 ARG cc_start: 0.6777 (mpp-170) cc_final: 0.6219 (mpp80) REVERT: A 381 GLN cc_start: 0.4055 (OUTLIER) cc_final: 0.3813 (tt0) REVERT: A 410 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.6090 (mtm) REVERT: A 423 LYS cc_start: 0.7483 (mmmt) cc_final: 0.7257 (mmmm) REVERT: A 478 GLN cc_start: 0.7257 (tt0) cc_final: 0.6322 (mp10) REVERT: A 567 ARG cc_start: 0.8015 (tpt90) cc_final: 0.7110 (tpp80) REVERT: A 603 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8196 (tt) REVERT: A 708 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8269 (mptt) REVERT: A 874 ASN cc_start: 0.7467 (m-40) cc_final: 0.7068 (m-40) REVERT: A 875 GLU cc_start: 0.7455 (tp30) cc_final: 0.7114 (tp30) REVERT: A 973 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: A 1174 TRP cc_start: 0.7076 (t-100) cc_final: 0.6757 (t60) REVERT: A 1180 LYS cc_start: 0.5365 (mmtt) cc_final: 0.4822 (pttp) REVERT: A 1191 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7376 (ttp-110) REVERT: A 1239 MET cc_start: 0.3605 (ptt) cc_final: 0.2742 (mtp) REVERT: A 1243 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8231 (mt) REVERT: A 1263 MET cc_start: 0.7659 (ppp) cc_final: 0.7316 (pp-130) REVERT: A 1316 GLN cc_start: 0.4818 (OUTLIER) cc_final: 0.4437 (pp30) REVERT: A 1581 GLU cc_start: 0.7023 (tp30) cc_final: 0.6760 (tt0) REVERT: A 1624 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: B 8 ARG cc_start: 0.7200 (mtt180) cc_final: 0.6151 (mmp-170) REVERT: B 20 THR cc_start: 0.7611 (p) cc_final: 0.7384 (p) REVERT: B 59 GLN cc_start: 0.7336 (mm110) cc_final: 0.6977 (mt0) REVERT: B 120 TRP cc_start: 0.6355 (p-90) cc_final: 0.5939 (p-90) REVERT: B 197 LYS cc_start: 0.8338 (tttt) cc_final: 0.7862 (tppt) REVERT: B 272 LYS cc_start: 0.7380 (mtmt) cc_final: 0.6480 (mtmt) REVERT: B 325 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6935 (tp30) REVERT: B 337 LYS cc_start: 0.7293 (mppt) cc_final: 0.6778 (mttm) REVERT: B 436 THR cc_start: 0.8819 (m) cc_final: 0.8595 (p) REVERT: B 481 MET cc_start: 0.7864 (mtt) cc_final: 0.7521 (mtm) REVERT: B 548 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7479 (mmm160) REVERT: B 550 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7719 (m-10) REVERT: B 562 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7972 (tmm) REVERT: B 593 MET cc_start: 0.8491 (ttp) cc_final: 0.8215 (ttm) REVERT: B 659 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: B 777 GLU cc_start: 0.8217 (tt0) cc_final: 0.7812 (pt0) REVERT: B 797 LYS cc_start: 0.7928 (ttpt) cc_final: 0.7276 (mmpt) REVERT: B 842 LYS cc_start: 0.8084 (ptpt) cc_final: 0.7467 (mmtt) REVERT: B 857 ASN cc_start: 0.8912 (p0) cc_final: 0.8679 (p0) REVERT: B 923 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.8236 (mtt180) REVERT: B 1018 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.6393 (mtp180) REVERT: B 1068 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.6484 (p90) REVERT: C 243 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6858 (pm20) REVERT: C 293 LEU cc_start: 0.7666 (mt) cc_final: 0.7382 (pp) REVERT: C 295 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.7990 (mmtt) REVERT: E 143 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7715 (pt0) REVERT: H 37 MET cc_start: 0.7895 (mtp) cc_final: 0.7670 (mtm) REVERT: I 29 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5782 (tp) REVERT: K 79 LYS cc_start: 0.8569 (ptpt) cc_final: 0.7923 (pttp) REVERT: N 63 LEU cc_start: 0.2449 (OUTLIER) cc_final: 0.2151 (mm) REVERT: N 83 LEU cc_start: 0.7039 (mt) cc_final: 0.6587 (mm) REVERT: N 94 LEU cc_start: 0.5273 (OUTLIER) cc_final: 0.5027 (pt) REVERT: N 116 ARG cc_start: 0.4218 (OUTLIER) cc_final: 0.3508 (ttt90) REVERT: M 39 MET cc_start: 0.4063 (OUTLIER) cc_final: 0.3650 (ppp) outliers start: 122 outliers final: 66 residues processed: 545 average time/residue: 0.7399 time to fit residues: 481.0044 Evaluate side-chains 531 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 441 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1646 ASP Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1068 HIS Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain M residue 39 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 304 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 310 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 305 optimal weight: 0.9980 chunk 375 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN A1118 GLN ** A1584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS B 972 ASN C 143 GLN E 210 GLN H 44 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.174620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.133731 restraints weight = 36637.151| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.82 r_work: 0.3360 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33872 Z= 0.151 Angle : 0.654 11.429 45959 Z= 0.337 Chirality : 0.046 0.219 5093 Planarity : 0.005 0.061 5797 Dihedral : 11.808 176.027 4980 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.67 % Favored : 92.30 % Rotamer: Outliers : 3.39 % Allowed : 23.00 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.43 (0.13), residues: 4001 helix: 0.20 (0.15), residues: 1239 sheet: -1.07 (0.20), residues: 669 loop : -1.62 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 140 TYR 0.028 0.001 TYR A 754 PHE 0.018 0.001 PHE I 19 TRP 0.018 0.001 TRP A 9 HIS 0.007 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (33855) covalent geometry : angle 0.65000 / 0.34 (45947) hydrogen bonds : bond 0.04336 / 2.88 ( 1035) hydrogen bonds : angle 4.64318 / 3.27 ( 2849) metal coordination : bond 0.00363 / 0.23 ( 17) metal coordination : angle 4.51691 / 2.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 451 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7544 (mtmt) cc_final: 0.6837 (mmtt) REVERT: A 127 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6958 (mt) REVERT: A 170 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.5955 (mp10) REVERT: A 200 MET cc_start: 0.8872 (tpt) cc_final: 0.8469 (mmp) REVERT: A 204 ARG cc_start: 0.6805 (mpp-170) cc_final: 0.6247 (mpp80) REVERT: A 410 MET cc_start: 0.6529 (OUTLIER) cc_final: 0.6162 (mtm) REVERT: A 422 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 423 LYS cc_start: 0.7441 (mmmt) cc_final: 0.7184 (mmmm) REVERT: A 478 GLN cc_start: 0.7326 (tt0) cc_final: 0.6392 (mp10) REVERT: A 512 MET cc_start: 0.6973 (tpp) cc_final: 0.6713 (tpt) REVERT: A 521 GLN cc_start: 0.6895 (mm-40) cc_final: 0.6679 (mp10) REVERT: A 567 ARG cc_start: 0.8125 (tpt90) cc_final: 0.7237 (tpp80) REVERT: A 603 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8132 (tt) REVERT: A 635 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.7193 (mpp) REVERT: A 708 LYS cc_start: 0.8830 (mtpp) cc_final: 0.8476 (mtpp) REVERT: A 874 ASN cc_start: 0.7551 (m-40) cc_final: 0.7111 (m-40) REVERT: A 875 GLU cc_start: 0.7512 (tp30) cc_final: 0.7166 (tp30) REVERT: A 973 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7613 (pt0) REVERT: A 1174 TRP cc_start: 0.7143 (t-100) cc_final: 0.6823 (t60) REVERT: A 1180 LYS cc_start: 0.5391 (mmtt) cc_final: 0.4678 (ttpp) REVERT: A 1191 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7496 (ttp-110) REVERT: A 1239 MET cc_start: 0.3631 (ptt) cc_final: 0.2751 (mtp) REVERT: A 1263 MET cc_start: 0.7673 (ppp) cc_final: 0.7352 (pp-130) REVERT: A 1316 GLN cc_start: 0.4852 (OUTLIER) cc_final: 0.4482 (pp30) REVERT: A 1342 MET cc_start: 0.4017 (OUTLIER) cc_final: 0.3210 (mmt) REVERT: A 1581 GLU cc_start: 0.7028 (tp30) cc_final: 0.6744 (tt0) REVERT: A 1624 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: B 8 ARG cc_start: 0.7208 (mtt180) cc_final: 0.6213 (mmp-170) REVERT: B 20 THR cc_start: 0.7688 (p) cc_final: 0.7448 (p) REVERT: B 59 GLN cc_start: 0.7392 (mm110) cc_final: 0.7071 (mt0) REVERT: B 120 TRP cc_start: 0.6406 (p-90) cc_final: 0.5993 (p-90) REVERT: B 197 LYS cc_start: 0.8372 (tttt) cc_final: 0.7905 (tppt) REVERT: B 272 LYS cc_start: 0.7406 (mtmt) cc_final: 0.6554 (mtmt) REVERT: B 320 ASN cc_start: 0.7512 (m-40) cc_final: 0.7074 (m-40) REVERT: B 325 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6985 (tp30) REVERT: B 337 LYS cc_start: 0.7294 (mppt) cc_final: 0.6806 (mttm) REVERT: B 436 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8560 (p) REVERT: B 481 MET cc_start: 0.7891 (mtt) cc_final: 0.7550 (mtm) REVERT: B 548 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7454 (mmm160) REVERT: B 550 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.7815 (m-10) REVERT: B 562 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8109 (tmm) REVERT: B 593 MET cc_start: 0.8567 (ttp) cc_final: 0.8305 (ttm) REVERT: B 659 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: B 777 GLU cc_start: 0.8213 (tt0) cc_final: 0.7828 (pt0) REVERT: B 797 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7314 (mmtt) REVERT: B 842 LYS cc_start: 0.8122 (ptpt) cc_final: 0.7501 (mmtt) REVERT: B 857 ASN cc_start: 0.8952 (p0) cc_final: 0.8684 (p0) REVERT: B 1018 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.6437 (mtp180) REVERT: B 1068 HIS cc_start: 0.7617 (OUTLIER) cc_final: 0.6462 (p90) REVERT: C 243 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6914 (pm20) REVERT: C 293 LEU cc_start: 0.7731 (mt) cc_final: 0.7498 (pp) REVERT: C 295 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.7975 (mmtt) REVERT: E 143 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7780 (pt0) REVERT: H 37 MET cc_start: 0.7974 (mtp) cc_final: 0.7684 (mtm) REVERT: H 54 ASP cc_start: 0.7513 (m-30) cc_final: 0.7237 (m-30) REVERT: I 17 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6323 (mt) REVERT: I 29 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5851 (tp) REVERT: K 79 LYS cc_start: 0.8607 (ptpt) cc_final: 0.7901 (pttp) REVERT: K 119 LYS cc_start: 0.7637 (tmtt) cc_final: 0.7380 (tmtm) REVERT: N 63 LEU cc_start: 0.2468 (OUTLIER) cc_final: 0.2168 (mm) REVERT: N 83 LEU cc_start: 0.7121 (mt) cc_final: 0.6670 (mm) REVERT: N 94 LEU cc_start: 0.5314 (OUTLIER) cc_final: 0.5041 (pt) REVERT: N 116 ARG cc_start: 0.4288 (OUTLIER) cc_final: 0.3575 (ttt90) outliers start: 120 outliers final: 66 residues processed: 536 average time/residue: 0.7429 time to fit residues: 474.2294 Evaluate side-chains 527 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 436 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1342 MET Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1646 ASP Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1068 HIS Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 137 optimal weight: 0.3980 chunk 200 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 398 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 330 optimal weight: 7.9990 chunk 251 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 248 optimal weight: 8.9990 chunk 217 optimal weight: 0.8980 chunk 101 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1584 ASN B 237 ASN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS C 143 GLN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN E 210 GLN H 44 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.177111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136541 restraints weight = 36791.316| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.81 r_work: 0.3402 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33872 Z= 0.123 Angle : 0.630 11.936 45959 Z= 0.325 Chirality : 0.044 0.198 5093 Planarity : 0.005 0.061 5797 Dihedral : 11.703 178.296 4977 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.92 % Favored : 93.05 % Rotamer: Outliers : 2.99 % Allowed : 23.57 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.26 (0.13), residues: 4001 helix: 0.38 (0.15), residues: 1232 sheet: -0.97 (0.20), residues: 635 loop : -1.55 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A1122 TYR 0.026 0.001 TYR A 754 PHE 0.020 0.001 PHE I 19 TRP 0.019 0.001 TRP A 9 HIS 0.005 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (33855) covalent geometry : angle 0.62636 / 0.32 (45947) hydrogen bonds : bond 0.03988 / 2.68 ( 1035) hydrogen bonds : angle 4.57527 / 3.23 ( 2849) metal coordination : bond 0.00317 / 0.19 ( 17) metal coordination : angle 4.34558 / 2.02 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 459 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7522 (mtmt) cc_final: 0.6795 (mmtt) REVERT: A 127 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6782 (mt) REVERT: A 200 MET cc_start: 0.8879 (tpt) cc_final: 0.8503 (mmp) REVERT: A 204 ARG cc_start: 0.6755 (mpp-170) cc_final: 0.6206 (mpp80) REVERT: A 341 LEU cc_start: 0.5440 (tp) cc_final: 0.5177 (tt) REVERT: A 422 GLU cc_start: 0.7603 (tm-30) cc_final: 0.6854 (pp20) REVERT: A 478 GLN cc_start: 0.7329 (tt0) cc_final: 0.6457 (mp10) REVERT: A 567 ARG cc_start: 0.8079 (tpt90) cc_final: 0.7146 (tpp80) REVERT: A 603 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8181 (tt) REVERT: A 635 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.7543 (mpp) REVERT: A 708 LYS cc_start: 0.8863 (mtpp) cc_final: 0.8366 (mptt) REVERT: A 874 ASN cc_start: 0.7509 (m-40) cc_final: 0.7084 (m-40) REVERT: A 875 GLU cc_start: 0.7575 (tp30) cc_final: 0.7233 (tp30) REVERT: A 973 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7555 (pt0) REVERT: A 993 ILE cc_start: 0.8697 (mt) cc_final: 0.8477 (mm) REVERT: A 1174 TRP cc_start: 0.7160 (t-100) cc_final: 0.6832 (t60) REVERT: A 1180 LYS cc_start: 0.5155 (OUTLIER) cc_final: 0.4554 (ttpp) REVERT: A 1191 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7388 (ttp-110) REVERT: A 1239 MET cc_start: 0.3731 (ptt) cc_final: 0.2790 (mtp) REVERT: A 1258 ASN cc_start: 0.8370 (m110) cc_final: 0.7889 (p0) REVERT: A 1263 MET cc_start: 0.7560 (ppp) cc_final: 0.7232 (pp-130) REVERT: A 1316 GLN cc_start: 0.4832 (OUTLIER) cc_final: 0.4420 (pp30) REVERT: A 1342 MET cc_start: 0.3949 (OUTLIER) cc_final: 0.3671 (mmp) REVERT: A 1581 GLU cc_start: 0.6961 (tp30) cc_final: 0.6636 (tt0) REVERT: A 1624 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: B 8 ARG cc_start: 0.7239 (mtt180) cc_final: 0.6191 (mmp-170) REVERT: B 20 THR cc_start: 0.7566 (p) cc_final: 0.7341 (p) REVERT: B 59 GLN cc_start: 0.7425 (mm110) cc_final: 0.7092 (mt0) REVERT: B 120 TRP cc_start: 0.6388 (p-90) cc_final: 0.5888 (p-90) REVERT: B 197 LYS cc_start: 0.8338 (tttt) cc_final: 0.7850 (tppt) REVERT: B 272 LYS cc_start: 0.7334 (mtmt) cc_final: 0.6439 (mtmt) REVERT: B 306 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7495 (mm-30) REVERT: B 320 ASN cc_start: 0.7452 (m-40) cc_final: 0.7049 (m-40) REVERT: B 325 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7024 (tp30) REVERT: B 337 LYS cc_start: 0.7157 (mppt) cc_final: 0.6711 (mttm) REVERT: B 436 THR cc_start: 0.8773 (m) cc_final: 0.8561 (p) REVERT: B 481 MET cc_start: 0.7856 (mtt) cc_final: 0.7525 (mtm) REVERT: B 548 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7404 (mmm160) REVERT: B 550 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7686 (m-10) REVERT: B 562 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7964 (tmm) REVERT: B 593 MET cc_start: 0.8476 (ttp) cc_final: 0.8208 (ttm) REVERT: B 659 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8525 (tm-30) REVERT: B 777 GLU cc_start: 0.8108 (tt0) cc_final: 0.7748 (pt0) REVERT: B 797 LYS cc_start: 0.7893 (ttpt) cc_final: 0.7292 (mmtt) REVERT: B 842 LYS cc_start: 0.8060 (ptpt) cc_final: 0.7488 (mmtt) REVERT: B 857 ASN cc_start: 0.8904 (p0) cc_final: 0.8650 (p0) REVERT: B 1018 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.6438 (mtp180) REVERT: B 1068 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.6481 (p90) REVERT: C 243 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7016 (pm20) REVERT: C 295 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8034 (mmtt) REVERT: E 116 GLN cc_start: 0.7642 (tp-100) cc_final: 0.7412 (tp40) REVERT: E 143 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7744 (pt0) REVERT: E 174 GLN cc_start: 0.8522 (mm110) cc_final: 0.8179 (mm110) REVERT: H 37 MET cc_start: 0.7949 (mtp) cc_final: 0.7707 (mtm) REVERT: H 38 ASP cc_start: 0.8022 (m-30) cc_final: 0.7756 (m-30) REVERT: H 54 ASP cc_start: 0.7466 (m-30) cc_final: 0.7173 (m-30) REVERT: I 17 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6364 (mt) REVERT: K 46 GLU cc_start: 0.8078 (mp0) cc_final: 0.7827 (mp0) REVERT: K 77 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7074 (mp0) REVERT: K 79 LYS cc_start: 0.8584 (ptpt) cc_final: 0.8281 (ptpt) REVERT: N 63 LEU cc_start: 0.2458 (OUTLIER) cc_final: 0.2159 (mm) REVERT: N 83 LEU cc_start: 0.7106 (mt) cc_final: 0.6657 (mm) REVERT: N 94 LEU cc_start: 0.5305 (OUTLIER) cc_final: 0.5051 (pt) REVERT: N 116 ARG cc_start: 0.4376 (OUTLIER) cc_final: 0.3606 (ttt90) outliers start: 106 outliers final: 59 residues processed: 533 average time/residue: 0.7162 time to fit residues: 454.2792 Evaluate side-chains 521 residues out of total 3544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 440 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1342 MET Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1646 ASP Chi-restraints excluded: chain A residue 1651 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1068 HIS Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 357 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 339 optimal weight: 0.8980 chunk 257 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 359 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1584 ASN B 580 HIS E 116 GLN E 210 GLN H 44 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.175024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134766 restraints weight = 36622.027| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.83 r_work: 0.3364 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33872 Z= 0.163 Angle : 0.660 12.233 45959 Z= 0.338 Chirality : 0.046 0.198 5093 Planarity : 0.005 0.062 5797 Dihedral : 11.646 178.957 4972 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.47 % Favored : 92.50 % Rotamer: Outliers : 3.10 % Allowed : 23.77 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.27 (0.13), residues: 4001 helix: 0.34 (0.15), residues: 1235 sheet: -0.98 (0.20), residues: 663 loop : -1.53 (0.14), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 140 TYR 0.034 0.002 TYR B 303 PHE 0.020 0.001 PHE I 19 TRP 0.018 0.001 TRP A 9 HIS 0.006 0.001 HIS A 995 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (33855) covalent geometry : angle 0.65697 / 0.34 (45947) hydrogen bonds : bond 0.04328 / 2.87 ( 1035) hydrogen bonds : angle 4.62244 / 3.25 ( 2849) metal coordination : bond 0.00395 / 0.24 ( 17) metal coordination : angle 4.19820 / 2.03 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14757.59 seconds wall clock time: 251 minutes 14.01 seconds (15074.01 seconds total)