Starting phenix.real_space_refine on Sun Feb 8 10:19:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sgl_25113/02_2026/7sgl_25113.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgl_25113/02_2026/7sgl_25113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sgl_25113/02_2026/7sgl_25113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgl_25113/02_2026/7sgl_25113.map" model { file = "/net/cci-nas-00/data/ceres_data/7sgl_25113/02_2026/7sgl_25113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgl_25113/02_2026/7sgl_25113.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 74 5.49 5 Mg 3 5.21 5 S 264 5.16 5 C 28365 2.51 5 N 7583 2.21 5 O 8414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44704 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 30853 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3852, 30804 Classifications: {'peptide': 3852} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 168, 'TRANS': 3682} Chain breaks: 11 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'TPO:plan-1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 3852, 30804 Classifications: {'peptide': 3852} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 168, 'TRANS': 3682} Chain breaks: 11 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'TPO:plan-1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 31388 Chain: "B" Number of atoms: 4102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4102 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 28, 'TRANS': 478} Chain: "C" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5099 Classifications: {'peptide': 631} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 603} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3311 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 406, 3299 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 25, 'TRANS': 380} Conformer: "B" Number of residues, atoms: 406, 3299 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 25, 'TRANS': 380} bond proxies already assigned to first conformer: 3370 Chain: "E" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1104 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 42128 SG CYS D 256 69.939 99.827 96.419 1.00 59.48 S ATOM 42270 SG CYS D 272 69.349 102.910 94.221 1.00 73.29 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ALYS A1000 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A1000 " occ=0.50 residue: pdb=" N AGLN A2838 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A2838 " occ=0.50 residue: pdb=" N AHIS A2865 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A2865 " occ=0.50 residue: pdb=" N AHIS A3903 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A3903 " occ=0.50 residue: pdb=" N APHE A4011 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A4011 " occ=0.50 residue: pdb=" N ATYR D 391 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 391 " occ=0.50 Time building chain proxies: 14.63, per 1000 atoms: 0.33 Number of scatterers: 44704 At special positions: 0 Unit cell: (144.109, 161.602, 248.234, 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 1 29.99 S 264 16.00 P 74 15.00 Mg 3 11.99 O 8414 8.00 N 7583 7.00 C 28365 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: 3.68 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 803 " pdb="ZN ZN D 803 " - pdb=" ND1 HIS D 254 " pdb="ZN ZN D 803 " - pdb=" ND1 HIS D 228 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 256 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 272 " Number of angles added : 2 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10346 Finding SS restraints... Secondary structure from input PDB file: 283 helices and 23 sheets defined 63.3% alpha, 6.2% beta 29 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 6.52 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 removed outlier: 3.609A pdb=" N CYS A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 45 removed outlier: 3.515A pdb=" N LEU A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.665A pdb=" N PHE A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 73 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 78 through 96 Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.963A pdb=" N LEU A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.634A pdb=" N MET A 144 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 145 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 146 " --> pdb=" O LEU A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 141 through 146' Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 167 through 185 removed outlier: 3.623A pdb=" N LYS A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 removed outlier: 4.054A pdb=" N ILE A 190 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 removed outlier: 3.598A pdb=" N ARG A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 241 through 257 removed outlier: 3.576A pdb=" N SER A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 289 through 302 removed outlier: 3.701A pdb=" N ALA A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 removed outlier: 3.737A pdb=" N ASN A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 351 removed outlier: 4.819A pdb=" N GLN A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 374 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 377 through 396 removed outlier: 4.385A pdb=" N PHE A 383 " --> pdb=" O LYS A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 450 through 469 removed outlier: 3.685A pdb=" N LEU A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 492 removed outlier: 4.381A pdb=" N CYS A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 538 through 546 Processing helix chain 'A' and resid 559 through 577 Processing helix chain 'A' and resid 616 through 634 Processing helix chain 'A' and resid 635 through 640 removed outlier: 3.674A pdb=" N GLN A 638 " --> pdb=" O PRO A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 660 Processing helix chain 'A' and resid 663 through 680 removed outlier: 4.240A pdb=" N TYR A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 722 through 736 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.502A pdb=" N ILE A 741 " --> pdb=" O PRO A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.530A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 796 through 801 removed outlier: 4.049A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 removed outlier: 4.390A pdb=" N ARG A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 884 removed outlier: 3.960A pdb=" N VAL A 884 " --> pdb=" O LYS A 881 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 881 through 884' Processing helix chain 'A' and resid 910 through 921 Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 958 through 974 removed outlier: 4.166A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 3.562A pdb=" N CYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 995 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1003 through 1017 Processing helix chain 'A' and resid 1023 through 1043 Processing helix chain 'A' and resid 1045 through 1052 removed outlier: 3.704A pdb=" N LYS A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1068 Processing helix chain 'A' and resid 1071 through 1090 removed outlier: 3.533A pdb=" N ARG A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ARG A1087 " --> pdb=" O ASN A1083 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLU A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1114 removed outlier: 5.882A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1117 No H-bonds generated for 'chain 'A' and resid 1115 through 1117' Processing helix chain 'A' and resid 1122 through 1141 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1164 through 1175 removed outlier: 3.681A pdb=" N LEU A1168 " --> pdb=" O CYS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1212 Processing helix chain 'A' and resid 1216 through 1225 removed outlier: 4.288A pdb=" N LEU A1220 " --> pdb=" O GLY A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1234 removed outlier: 3.540A pdb=" N SER A1233 " --> pdb=" O GLY A1230 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY A1234 " --> pdb=" O GLN A1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1230 through 1234' Processing helix chain 'A' and resid 1240 through 1244 removed outlier: 3.614A pdb=" N TYR A1243 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A1244 " --> pdb=" O LEU A1241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1240 through 1244' Processing helix chain 'A' and resid 1249 through 1273 removed outlier: 3.687A pdb=" N TRP A1256 " --> pdb=" O ALA A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1283 removed outlier: 3.523A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A1282 " --> pdb=" O ALA A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1301 Processing helix chain 'A' and resid 1305 through 1311 removed outlier: 4.090A pdb=" N ALA A1309 " --> pdb=" O ASP A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1352 removed outlier: 3.534A pdb=" N TYR A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1378 Processing helix chain 'A' and resid 1379 through 1382 Processing helix chain 'A' and resid 1388 through 1393 removed outlier: 3.629A pdb=" N MET A1392 " --> pdb=" O ASP A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 Processing helix chain 'A' and resid 1411 through 1423 Processing helix chain 'A' and resid 1424 through 1432 Processing helix chain 'A' and resid 1441 through 1462 removed outlier: 3.978A pdb=" N ARG A1445 " --> pdb=" O ALA A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1474 through 1490 Processing helix chain 'A' and resid 1504 through 1522 removed outlier: 3.539A pdb=" N GLN A1509 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A1512 " --> pdb=" O LYS A1508 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A1516 " --> pdb=" O SER A1512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A1521 " --> pdb=" O LEU A1517 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY A1522 " --> pdb=" O ALA A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1533 removed outlier: 3.620A pdb=" N LEU A1533 " --> pdb=" O VAL A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1563 removed outlier: 3.554A pdb=" N PHE A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1572 removed outlier: 3.962A pdb=" N ILE A1567 " --> pdb=" O PHE A1563 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN A1568 " --> pdb=" O SER A1564 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A1572 " --> pdb=" O ASN A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1585 removed outlier: 4.244A pdb=" N GLU A1581 " --> pdb=" O LEU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1607 Processing helix chain 'A' and resid 1611 through 1624 removed outlier: 4.352A pdb=" N GLY A1615 " --> pdb=" O GLN A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1630 removed outlier: 4.167A pdb=" N ASP A1630 " --> pdb=" O LYS A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 3.527A pdb=" N LYS A1642 " --> pdb=" O PRO A1638 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A1653 " --> pdb=" O LEU A1649 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A1654 " --> pdb=" O ALA A1650 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1680 removed outlier: 3.794A pdb=" N VAL A1671 " --> pdb=" O SER A1667 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A1673 " --> pdb=" O PRO A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1695 removed outlier: 3.781A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A1691 " --> pdb=" O HIS A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1696 through 1699 Processing helix chain 'A' and resid 1704 through 1722 removed outlier: 4.100A pdb=" N GLU A1708 " --> pdb=" O GLY A1704 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1754 Processing helix chain 'A' and resid 1758 through 1768 Processing helix chain 'A' and resid 1774 through 1789 removed outlier: 4.267A pdb=" N GLY A1789 " --> pdb=" O ILE A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1807 removed outlier: 3.521A pdb=" N GLN A1794 " --> pdb=" O SER A1790 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1830 removed outlier: 4.619A pdb=" N LEU A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR A1826 " --> pdb=" O ARG A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1852 removed outlier: 5.052A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1862 through 1882 removed outlier: 4.052A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) Processing helix chain 'A' and resid 1885 through 1891 removed outlier: 3.794A pdb=" N VAL A1889 " --> pdb=" O PRO A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1893 through 1900 removed outlier: 3.658A pdb=" N ASN A1897 " --> pdb=" O GLU A1893 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1924 Processing helix chain 'A' and resid 1933 through 1956 removed outlier: 4.248A pdb=" N VAL A1955 " --> pdb=" O VAL A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1958 through 1967 removed outlier: 3.740A pdb=" N TYR A1962 " --> pdb=" O GLU A1958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1998 through 2014 removed outlier: 3.598A pdb=" N LYS A2002 " --> pdb=" O MET A1998 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR A2004 " --> pdb=" O ARG A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2025 through 2029 Processing helix chain 'A' and resid 2035 through 2045 removed outlier: 4.221A pdb=" N GLN A2042 " --> pdb=" O GLU A2038 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N PHE A2043 " --> pdb=" O GLU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2107 removed outlier: 3.651A pdb=" N ARG A2106 " --> pdb=" O LYS A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2135 removed outlier: 3.786A pdb=" N ASN A2135 " --> pdb=" O GLY A2131 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 Processing helix chain 'A' and resid 2154 through 2159 removed outlier: 3.973A pdb=" N ARG A2158 " --> pdb=" O GLU A2155 " (cutoff:3.500A) Proline residue: A2159 - end of helix Processing helix chain 'A' and resid 2160 through 2174 removed outlier: 3.680A pdb=" N TRP A2164 " --> pdb=" O TYR A2160 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2183 through 2196 Processing helix chain 'A' and resid 2197 through 2199 No H-bonds generated for 'chain 'A' and resid 2197 through 2199' Processing helix chain 'A' and resid 2205 through 2222 Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2252 through 2261 Processing helix chain 'A' and resid 2268 through 2283 removed outlier: 4.303A pdb=" N VAL A2272 " --> pdb=" O LYS A2268 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY A2273 " --> pdb=" O ASP A2269 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2305 Processing helix chain 'A' and resid 2306 through 2309 Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 3.558A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2354 removed outlier: 3.884A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2358 through 2368 removed outlier: 3.791A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2371 through 2375 removed outlier: 3.570A pdb=" N LEU A2374 " --> pdb=" O PHE A2371 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2387 through 2389 No H-bonds generated for 'chain 'A' and resid 2387 through 2389' Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.725A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 Processing helix chain 'A' and resid 2419 through 2426 Processing helix chain 'A' and resid 2428 through 2443 Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2447 through 2459 Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2460 through 2464 removed outlier: 3.967A pdb=" N SER A2463 " --> pdb=" O GLU A2460 " (cutoff:3.500A) Processing helix chain 'A' and resid 2468 through 2484 removed outlier: 3.562A pdb=" N GLN A2472 " --> pdb=" O THR A2468 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2509 Processing helix chain 'A' and resid 2510 through 2512 No H-bonds generated for 'chain 'A' and resid 2510 through 2512' Processing helix chain 'A' and resid 2514 through 2526 Processing helix chain 'A' and resid 2534 through 2543 removed outlier: 4.142A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2546 No H-bonds generated for 'chain 'A' and resid 2544 through 2546' Processing helix chain 'A' and resid 2553 through 2564 Processing helix chain 'A' and resid 2565 through 2568 removed outlier: 3.516A pdb=" N MET A2568 " --> pdb=" O MET A2565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2565 through 2568' Processing helix chain 'A' and resid 2580 through 2584 removed outlier: 3.508A pdb=" N CYS A2584 " --> pdb=" O LEU A2581 " (cutoff:3.500A) Processing helix chain 'A' and resid 2593 through 2603 removed outlier: 3.766A pdb=" N PHE A2597 " --> pdb=" O SER A2593 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A2598 " --> pdb=" O ASP A2594 " (cutoff:3.500A) Processing helix chain 'A' and resid 2786 through 2799 removed outlier: 3.593A pdb=" N LEU A2790 " --> pdb=" O LYS A2786 " (cutoff:3.500A) Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2820 Processing helix chain 'A' and resid 2821 through 2823 No H-bonds generated for 'chain 'A' and resid 2821 through 2823' Processing helix chain 'A' and resid 2825 through 2846 Processing helix chain 'A' and resid 2851 through 2865 removed outlier: 3.793A pdb=" N AHIS A2865 " --> pdb=" O ILE A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2884 Processing helix chain 'A' and resid 2885 through 2900 Processing helix chain 'A' and resid 2917 through 2932 Processing helix chain 'A' and resid 2935 through 2946 Processing helix chain 'A' and resid 2950 through 2962 removed outlier: 3.655A pdb=" N GLN A2954 " --> pdb=" O LYS A2950 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2977 Processing helix chain 'A' and resid 2987 through 3005 Processing helix chain 'A' and resid 3007 through 3015 Processing helix chain 'A' and resid 3026 through 3032 Processing helix chain 'A' and resid 3033 through 3040 Processing helix chain 'A' and resid 3040 through 3054 Processing helix chain 'A' and resid 3059 through 3070 removed outlier: 3.581A pdb=" N HIS A3070 " --> pdb=" O ASP A3066 " (cutoff:3.500A) Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 3.897A pdb=" N ALA A3076 " --> pdb=" O GLU A3072 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A3077 " --> pdb=" O LEU A3073 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A3080 " --> pdb=" O ALA A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3082 through 3093 Processing helix chain 'A' and resid 3095 through 3115 Processing helix chain 'A' and resid 3121 through 3130 Processing helix chain 'A' and resid 3131 through 3147 removed outlier: 3.910A pdb=" N LYS A3147 " --> pdb=" O SER A3143 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3165 Processing helix chain 'A' and resid 3175 through 3198 removed outlier: 3.570A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3226 through 3249 removed outlier: 3.534A pdb=" N LEU A3230 " --> pdb=" O ASP A3226 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3267 removed outlier: 3.523A pdb=" N LEU A3262 " --> pdb=" O LEU A3258 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LYS A3264 " --> pdb=" O LYS A3260 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLU A3265 " --> pdb=" O GLU A3261 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A3267 " --> pdb=" O HIS A3263 " (cutoff:3.500A) Processing helix chain 'A' and resid 3270 through 3288 removed outlier: 3.565A pdb=" N VAL A3274 " --> pdb=" O ASP A3270 " (cutoff:3.500A) Processing helix chain 'A' and resid 3292 through 3308 removed outlier: 3.674A pdb=" N VAL A3297 " --> pdb=" O CYS A3293 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A3298 " --> pdb=" O SER A3294 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A3302 " --> pdb=" O LEU A3298 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR A3303 " --> pdb=" O THR A3299 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A3304 " --> pdb=" O VAL A3300 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER A3305 " --> pdb=" O LEU A3301 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU A3306 " --> pdb=" O LYS A3302 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3317 Processing helix chain 'A' and resid 3319 through 3344 Processing helix chain 'A' and resid 3345 through 3349 removed outlier: 3.796A pdb=" N LEU A3348 " --> pdb=" O PRO A3345 " (cutoff:3.500A) Processing helix chain 'A' and resid 3352 through 3364 removed outlier: 3.554A pdb=" N GLY A3364 " --> pdb=" O LEU A3360 " (cutoff:3.500A) Processing helix chain 'A' and resid 3369 through 3393 Processing helix chain 'A' and resid 3405 through 3430 removed outlier: 4.255A pdb=" N VAL A3409 " --> pdb=" O PRO A3405 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A3430 " --> pdb=" O LYS A3426 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 Processing helix chain 'A' and resid 3458 through 3463 Processing helix chain 'A' and resid 3464 through 3475 removed outlier: 3.744A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A3474 " --> pdb=" O GLN A3470 " (cutoff:3.500A) Processing helix chain 'A' and resid 3475 through 3487 removed outlier: 6.004A pdb=" N SER A3481 " --> pdb=" O GLU A3477 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU A3482 " --> pdb=" O GLU A3478 " (cutoff:3.500A) Processing helix chain 'A' and resid 3488 through 3490 No H-bonds generated for 'chain 'A' and resid 3488 through 3490' Processing helix chain 'A' and resid 3491 through 3497 removed outlier: 3.875A pdb=" N ILE A3496 " --> pdb=" O TRP A3493 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N SER A3497 " --> pdb=" O GLN A3494 " (cutoff:3.500A) Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3508 through 3510 No H-bonds generated for 'chain 'A' and resid 3508 through 3510' Processing helix chain 'A' and resid 3511 through 3525 removed outlier: 4.686A pdb=" N HIS A3516 " --> pdb=" O VAL A3512 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER A3517 " --> pdb=" O ALA A3513 " (cutoff:3.500A) Processing helix chain 'A' and resid 3526 through 3528 No H-bonds generated for 'chain 'A' and resid 3526 through 3528' Processing helix chain 'A' and resid 3529 through 3538 removed outlier: 3.893A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3563 removed outlier: 3.728A pdb=" N LYS A3550 " --> pdb=" O SER A3546 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3577 Processing helix chain 'A' and resid 3580 through 3598 removed outlier: 3.655A pdb=" N LYS A3586 " --> pdb=" O GLU A3582 " (cutoff:3.500A) Processing helix chain 'A' and resid 3602 through 3618 removed outlier: 3.640A pdb=" N ILE A3606 " --> pdb=" O ASN A3602 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3626 through 3637 removed outlier: 3.658A pdb=" N PHE A3632 " --> pdb=" O PHE A3628 " (cutoff:3.500A) Processing helix chain 'A' and resid 3638 through 3643 Processing helix chain 'A' and resid 3648 through 3653 Processing helix chain 'A' and resid 3655 through 3672 removed outlier: 3.540A pdb=" N ASP A3661 " --> pdb=" O SER A3657 " (cutoff:3.500A) Processing helix chain 'A' and resid 3679 through 3683 removed outlier: 3.525A pdb=" N GLU A3682 " --> pdb=" O ASN A3679 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS A3683 " --> pdb=" O LEU A3680 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3679 through 3683' Processing helix chain 'A' and resid 3684 through 3689 Processing helix chain 'A' and resid 3712 through 3716 Processing helix chain 'A' and resid 3758 through 3778 removed outlier: 3.589A pdb=" N GLN A3777 " --> pdb=" O GLY A3773 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A3778 " --> pdb=" O ILE A3774 " (cutoff:3.500A) Processing helix chain 'A' and resid 3778 through 3783 Processing helix chain 'A' and resid 3812 through 3818 Processing helix chain 'A' and resid 3821 through 3831 Processing helix chain 'A' and resid 3834 through 3848 removed outlier: 4.033A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3862 removed outlier: 3.973A pdb=" N MET A3856 " --> pdb=" O VAL A3852 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3876 removed outlier: 3.610A pdb=" N THR A3867 " --> pdb=" O ASN A3863 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A3876 " --> pdb=" O ARG A3872 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3890 Processing helix chain 'A' and resid 3893 through 3919 Processing helix chain 'A' and resid 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3947 through 3952 Processing helix chain 'A' and resid 3964 through 3971 removed outlier: 3.754A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 4.311A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3995 through 4007 Processing helix chain 'A' and resid 4012 through 4022 removed outlier: 3.556A pdb=" N PHE A4016 " --> pdb=" O ASP A4012 " (cutoff:3.500A) Processing helix chain 'A' and resid 4039 through 4053 removed outlier: 3.861A pdb=" N LYS A4043 " --> pdb=" O TYR A4039 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE A4044 " --> pdb=" O PRO A4040 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4068 Processing helix chain 'A' and resid 4073 through 4083 Processing helix chain 'A' and resid 4099 through 4112 Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4119 through 4120 No H-bonds generated for 'chain 'A' and resid 4119 through 4120' Processing helix chain 'A' and resid 4121 through 4125 Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.729A pdb=" N PHE B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 78 removed outlier: 3.975A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 121 removed outlier: 3.744A pdb=" N ILE B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 135 removed outlier: 3.976A pdb=" N LYS B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 155 Processing helix chain 'B' and resid 180 through 197 Processing helix chain 'B' and resid 216 through 220 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 332 through 337 removed outlier: 3.653A pdb=" N GLU B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 377 through 392 removed outlier: 4.030A pdb=" N LEU B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 470 removed outlier: 3.558A pdb=" N LEU B 469 " --> pdb=" O ILE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 Processing helix chain 'B' and resid 510 through 519 removed outlier: 3.569A pdb=" N ASN B 515 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 530 removed outlier: 4.022A pdb=" N GLU B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 29 through 48 Processing helix chain 'C' and resid 87 through 96 Processing helix chain 'C' and resid 106 through 122 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 198 through 217 removed outlier: 3.685A pdb=" N LEU C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU C 216 " --> pdb=" O MET C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.609A pdb=" N ARG C 232 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'C' and resid 349 through 351 No H-bonds generated for 'chain 'C' and resid 349 through 351' Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.673A pdb=" N PHE C 355 " --> pdb=" O GLN C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.661A pdb=" N ILE C 482 " --> pdb=" O THR C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 500 removed outlier: 3.784A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 516 removed outlier: 3.640A pdb=" N LEU C 516 " --> pdb=" O ILE C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 537 removed outlier: 3.708A pdb=" N THR C 523 " --> pdb=" O PRO C 519 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Proline residue: C 529 - end of helix Processing helix chain 'C' and resid 549 through 554 removed outlier: 3.551A pdb=" N ILE C 553 " --> pdb=" O THR C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 626 removed outlier: 4.069A pdb=" N ALA C 612 " --> pdb=" O SER C 608 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN C 615 " --> pdb=" O GLU C 611 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE C 620 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 621 " --> pdb=" O ILE C 617 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN C 622 " --> pdb=" O ASN C 618 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE C 623 " --> pdb=" O HIS C 619 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP C 625 " --> pdb=" O GLU C 621 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 626 " --> pdb=" O GLN C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 645 removed outlier: 3.942A pdb=" N ILE C 636 " --> pdb=" O PHE C 632 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP C 637 " --> pdb=" O MET C 633 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU C 645 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 648 No H-bonds generated for 'chain 'C' and resid 646 through 648' Processing helix chain 'C' and resid 651 through 669 removed outlier: 4.106A pdb=" N ASN C 656 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ASN C 657 " --> pdb=" O GLN C 653 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE C 658 " --> pdb=" O ARG C 654 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 661 " --> pdb=" O ASN C 657 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 667 " --> pdb=" O GLN C 663 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE C 668 " --> pdb=" O GLU C 664 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C 669 " --> pdb=" O LYS C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 731 removed outlier: 4.080A pdb=" N MET C 731 " --> pdb=" O ASP C 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 26 removed outlier: 3.688A pdb=" N ARG D 25 " --> pdb=" O GLU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 44 through 52 Processing helix chain 'D' and resid 62 through 72 removed outlier: 4.164A pdb=" N SER D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 79 removed outlier: 3.542A pdb=" N ARG D 76 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE D 77 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 149 removed outlier: 3.715A pdb=" N MET D 147 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU D 148 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 195 removed outlier: 3.516A pdb=" N CYS D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 224 Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 260 through 267 Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 321 through 333 Processing helix chain 'D' and resid 347 through 356 Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing sheet with id=AA1, first strand: chain 'D' and resid 173 through 175 removed outlier: 4.194A pdb=" N VAL A 514 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR D 301 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AA3, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA4, first strand: chain 'A' and resid 2634 through 2636 Processing sheet with id=AA5, first strand: chain 'A' and resid 3719 through 3722 Processing sheet with id=AA6, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 6.735A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 3809 through 3811 Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 109 removed outlier: 6.630A pdb=" N VAL B 85 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLU B 107 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU B 83 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ARG B 35 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ARG B 165 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER B 37 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N MET B 167 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 39 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE B 169 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU B 41 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N PHE B 199 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N MET B 203 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU B 168 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 257 through 262 removed outlier: 3.732A pdb=" N SER B 257 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 432 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 396 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL B 394 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY B 349 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG B 399 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 347 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR B 401 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU B 345 " --> pdb=" O THR B 401 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 286 through 289 removed outlier: 3.510A pdb=" N ILE C 311 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 297 through 304 removed outlier: 3.686A pdb=" N VAL C 294 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR C 295 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 325 through 329 removed outlier: 3.574A pdb=" N ILE B 327 " --> pdb=" O GLN B 320 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 375 through 376 Processing sheet with id=AB5, first strand: chain 'B' and resid 420 through 421 Processing sheet with id=AB6, first strand: chain 'C' and resid 77 through 84 removed outlier: 6.150A pdb=" N LEU C 56 " --> pdb=" O HIS C 80 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS C 82 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE C 54 " --> pdb=" O HIS C 82 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU C 53 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 10 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LYS C 7 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS C 129 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N SER C 160 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG C 130 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N GLN C 162 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 132 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHE C 164 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE C 134 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 247 through 252 removed outlier: 6.630A pdb=" N VAL C 361 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N GLN C 360 " --> pdb=" O GLN C 423 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLN C 423 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ALA C 366 " --> pdb=" O GLU C 417 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N GLU C 417 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS C 418 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N MET C 389 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 390 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE C 345 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE C 392 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 341 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N CYS C 339 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE C 340 " --> pdb=" O ARG C 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 464 through 467 removed outlier: 3.882A pdb=" N ASP C 467 " --> pdb=" O THR C 472 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR C 472 " --> pdb=" O ASP C 467 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 14 through 16 removed outlier: 6.655A pdb=" N SER D 15 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TYR D 29 " --> pdb=" O TYR D 60 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU D 59 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.525A pdb=" N GLY D 126 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY D 129 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR D 130 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N TYR D 163 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU D 132 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL D 162 " --> pdb=" O TYR D 338 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 151 through 152 removed outlier: 3.600A pdb=" N ARG D 155 " --> pdb=" O SER D 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 253 through 254 removed outlier: 8.312A pdb=" N HIS D 254 " --> pdb=" O HIS D 200 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL D 202 " --> pdb=" O HIS D 254 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 285 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N TYR D 312 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER D 286 " --> pdb=" O TYR D 312 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ALA D 314 " --> pdb=" O SER D 286 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS D 288 " --> pdb=" O ALA D 314 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER D 311 " --> pdb=" O THR D 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 227 through 228 removed outlier: 6.093A pdb=" N VAL D 227 " --> pdb=" O THR D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 276 through 277 removed outlier: 3.577A pdb=" N ARG D 277 " --> pdb=" O ILE D 280 " (cutoff:3.500A) 2276 hydrogen bonds defined for protein. 6623 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 16.53 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 7302 1.30 - 1.43: 11766 1.43 - 1.56: 26156 1.56 - 1.68: 135 1.68 - 1.81: 415 Bond restraints: 45774 Sorted by residual: bond pdb=" OG1 TPO A2645 " pdb=" P TPO A2645 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" OG1 TPO A2609 " pdb=" P TPO A2609 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" OG1 TPO A2638 " pdb=" P TPO A2638 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" OG1 TPO A2647 " pdb=" P TPO A2647 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" O1P TPO A2609 " pdb=" P TPO A2609 " ideal model delta sigma weight residual 1.525 1.611 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 45769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 61589 2.56 - 5.12: 502 5.12 - 7.69: 35 7.69 - 10.25: 13 10.25 - 12.81: 4 Bond angle restraints: 62143 Sorted by residual: angle pdb=" N LEU A 435 " pdb=" CA LEU A 435 " pdb=" C LEU A 435 " ideal model delta sigma weight residual 111.07 120.87 -9.80 1.07e+00 8.73e-01 8.39e+01 angle pdb=" PB ATP A4201 " pdb=" O3B ATP A4201 " pdb=" PG ATP A4201 " ideal model delta sigma weight residual 139.87 131.95 7.92 1.00e+00 1.00e+00 6.27e+01 angle pdb=" N SER A1823 " pdb=" CA SER A1823 " pdb=" C SER A1823 " ideal model delta sigma weight residual 111.24 121.39 -10.15 1.29e+00 6.01e-01 6.19e+01 angle pdb=" C VAL A 434 " pdb=" CA VAL A 434 " pdb=" CB VAL A 434 " ideal model delta sigma weight residual 111.29 121.77 -10.48 1.64e+00 3.72e-01 4.08e+01 angle pdb=" C ARG A1822 " pdb=" CA ARG A1822 " pdb=" CB ARG A1822 " ideal model delta sigma weight residual 110.56 119.86 -9.30 1.83e+00 2.99e-01 2.59e+01 ... (remaining 62138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 26693 24.87 - 49.74: 869 49.74 - 74.61: 218 74.61 - 99.48: 61 99.48 - 124.36: 10 Dihedral angle restraints: 27851 sinusoidal: 11948 harmonic: 15903 Sorted by residual: dihedral pdb=" C VAL A 434 " pdb=" N VAL A 434 " pdb=" CA VAL A 434 " pdb=" CB VAL A 434 " ideal model delta harmonic sigma weight residual -122.00 -135.74 13.74 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" CA LYS A 722 " pdb=" C LYS A 722 " pdb=" N ASP A 723 " pdb=" CA ASP A 723 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" O12 IHP B 701 " pdb=" C2 IHP B 701 " pdb=" C3 IHP B 701 " pdb=" O13 IHP B 701 " ideal model delta sinusoidal sigma weight residual 64.08 -60.28 124.36 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 27848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.015: 6959 1.015 - 2.030: 0 2.030 - 3.044: 0 3.044 - 4.059: 0 4.059 - 5.074: 3 Chirality restraints: 6962 Sorted by residual: chirality pdb=" C4 IHP B 701 " pdb=" C3 IHP B 701 " pdb=" C5 IHP B 701 " pdb=" O14 IHP B 701 " both_signs ideal model delta sigma weight residual False 2.48 -2.59 5.07 2.00e-01 2.50e+01 6.44e+02 chirality pdb=" C2 IHP B 701 " pdb=" C1 IHP B 701 " pdb=" C3 IHP B 701 " pdb=" O12 IHP B 701 " both_signs ideal model delta sigma weight residual False -2.52 2.47 -4.98 2.00e-01 2.50e+01 6.21e+02 chirality pdb=" C1 IHP B 701 " pdb=" C2 IHP B 701 " pdb=" C6 IHP B 701 " pdb=" O11 IHP B 701 " both_signs ideal model delta sigma weight residual False 2.32 -2.57 4.89 2.00e-01 2.50e+01 5.97e+02 ... (remaining 6959 not shown) Planarity restraints: 7706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA E 46 " 0.041 2.00e-02 2.50e+03 1.95e-02 1.04e+01 pdb=" N9 DA E 46 " -0.046 2.00e-02 2.50e+03 pdb=" C8 DA E 46 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DA E 46 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DA E 46 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA E 46 " 0.009 2.00e-02 2.50e+03 pdb=" N6 DA E 46 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA E 46 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA E 46 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA E 46 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DA E 46 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG E 13 " 0.006 2.00e-02 2.50e+03 1.55e-02 7.16e+00 pdb=" N9 DG E 13 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DG E 13 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DG E 13 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG E 13 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG E 13 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG E 13 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG E 13 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DG E 13 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG E 13 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG E 13 " -0.023 2.00e-02 2.50e+03 pdb=" C4 DG E 13 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA E 14 " 0.025 2.00e-02 2.50e+03 1.58e-02 6.85e+00 pdb=" N9 DA E 14 " -0.041 2.00e-02 2.50e+03 pdb=" C8 DA E 14 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DA E 14 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DA E 14 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA E 14 " 0.007 2.00e-02 2.50e+03 pdb=" N6 DA E 14 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA E 14 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DA E 14 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA E 14 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA E 14 " -0.006 2.00e-02 2.50e+03 ... (remaining 7703 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 158 2.49 - 3.09: 31780 3.09 - 3.69: 67215 3.69 - 4.30: 100620 4.30 - 4.90: 163967 Nonbonded interactions: 363740 Sorted by model distance: nonbonded pdb=" OP1 DA E 25 " pdb="MG MG D 802 " model vdw 1.886 2.170 nonbonded pdb=" OD1 ASN A3927 " pdb="MG MG A4200 " model vdw 2.066 2.170 nonbonded pdb=" OD2 ASP A3941 " pdb="MG MG A4200 " model vdw 2.113 2.170 nonbonded pdb=" CD2 HIS D 38 " pdb="MG MG D 801 " model vdw 2.116 2.390 nonbonded pdb=" O ASN A2152 " pdb=" OD1 ASN A2152 " model vdw 2.173 3.040 ... (remaining 363735 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=0.50 max=1.00 mean=1.00 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: 10.130 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: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 63.050 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.209 45778 Z= 0.309 Angle : 0.598 16.010 62145 Z= 0.354 Chirality : 0.112 5.074 6962 Planarity : 0.003 0.039 7706 Dihedral : 13.502 124.356 17505 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.24 % Allowed : 4.34 % Favored : 94.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.41 % 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: -1.62 (0.11), residues: 5367 helix: -0.18 (0.09), residues: 3008 sheet: -1.75 (0.28), residues: 296 loop : -2.27 (0.12), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1735 TYR 0.011 0.001 TYR A2316 PHE 0.020 0.001 PHE A1923 TRP 0.006 0.001 TRP D 78 HIS 0.003 0.000 HIS D 33 Details of bonding type rmsd covalent geometry : bond 0.00635 (45774) covalent geometry : angle 0.59415 (62143) hydrogen bonds : bond 0.15059 ( 2345) hydrogen bonds : angle 5.51362 ( 6765) metal coordination : bond 0.18110 ( 4) metal coordination : angle 11.92606 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 511 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5178 (tpp) cc_final: 0.4977 (tmm) REVERT: A 408 TYR cc_start: 0.8300 (m-80) cc_final: 0.7847 (m-80) REVERT: A 1356 TRP cc_start: 0.7913 (p-90) cc_final: 0.7465 (p-90) REVERT: A 1362 ASP cc_start: 0.6882 (m-30) cc_final: 0.6538 (t0) REVERT: A 1592 MET cc_start: 0.8096 (tpt) cc_final: 0.7796 (tpt) REVERT: A 1625 HIS cc_start: 0.7743 (m90) cc_final: 0.7405 (m90) REVERT: A 1626 TRP cc_start: 0.7014 (m100) cc_final: 0.6548 (m100) REVERT: A 1668 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.5656 (t80) REVERT: A 1744 LYS cc_start: 0.8978 (ptpp) cc_final: 0.8435 (tppp) REVERT: A 1824 LEU cc_start: 0.8880 (tt) cc_final: 0.8590 (mp) REVERT: A 1829 TRP cc_start: 0.8595 (m100) cc_final: 0.8275 (m100) REVERT: A 1871 MET cc_start: 0.8096 (ptp) cc_final: 0.7715 (ptm) REVERT: A 1913 LYS cc_start: 0.8903 (tttt) cc_final: 0.8690 (tptt) REVERT: A 1927 MET cc_start: 0.7593 (mtp) cc_final: 0.7228 (mpm) REVERT: A 1933 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.7932 (mm) REVERT: A 1993 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: A 2094 MET cc_start: 0.8192 (tpt) cc_final: 0.7953 (tpt) REVERT: A 2097 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8737 (mt) REVERT: A 2437 ASP cc_start: 0.8222 (m-30) cc_final: 0.7953 (m-30) REVERT: A 3414 MET cc_start: 0.8515 (mmm) cc_final: 0.8167 (mmm) REVERT: A 3607 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8125 (pt0) REVERT: A 3609 MET cc_start: 0.8278 (mmt) cc_final: 0.8023 (mmp) REVERT: C 730 ASP cc_start: 0.7622 (t70) cc_final: 0.7336 (m-30) outliers start: 59 outliers final: 15 residues processed: 565 average time/residue: 0.9152 time to fit residues: 621.7878 Evaluate side-chains 279 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 259 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2899 ARG Chi-restraints excluded: chain A residue 3077 ILE Chi-restraints excluded: chain A residue 3544 ASP Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3607 GLU Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 19 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 0.0970 chunk 223 optimal weight: 2.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 191 ASN A 278 HIS A 281 GLN A 325 ASN A 377 ASN A 399 GLN A 409 GLN A 415 GLN A 442 GLN A 485 GLN A 562 HIS A 625 ASN A 857 GLN A 935 HIS A1004 GLN A1043 GLN A1222 ASN A1251 GLN A1287 GLN A1418 HIS A1435 ASN A1442 GLN A1477 HIS ** A1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1737 ASN A1772 HIS A1779 GLN A1794 GLN A1941 HIS A1946 ASN A2225 HIS A2508 GLN A2784 GLN A2799 GLN A2834 GLN A2859 GLN A2885 GLN A3112 GLN A3139 GLN A3166 ASN A3278 GLN A3383 GLN A3515 GLN A3787 GLN A3818 ASN A3850 HIS A3944 HIS A3951 GLN A3966 GLN A3986 HIS A4000 ASN A4018 GLN A4110 GLN B 95 ASN B 359 HIS B 426 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN C 423 GLN C 440 ASN C 514 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.100732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.067172 restraints weight = 288435.831| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 4.53 r_work: 0.2958 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 45778 Z= 0.171 Angle : 0.607 12.929 62145 Z= 0.307 Chirality : 0.042 0.324 6962 Planarity : 0.004 0.042 7706 Dihedral : 12.956 90.749 6634 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.03 % Allowed : 9.82 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % 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: -0.36 (0.11), residues: 5367 helix: 0.81 (0.09), residues: 3047 sheet: -1.20 (0.29), residues: 272 loop : -1.71 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A3833 TYR 0.032 0.001 TYR A1873 PHE 0.029 0.002 PHE A2260 TRP 0.037 0.001 TRP D 267 HIS 0.008 0.001 HIS A2225 Details of bonding type rmsd covalent geometry : bond 0.00404 (45774) covalent geometry : angle 0.60596 (62143) hydrogen bonds : bond 0.04156 ( 2345) hydrogen bonds : angle 4.23832 ( 6765) metal coordination : bond 0.00749 ( 4) metal coordination : angle 5.51860 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 275 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5056 (tpp) cc_final: 0.4699 (tmm) REVERT: A 408 TYR cc_start: 0.8704 (m-80) cc_final: 0.8412 (m-80) REVERT: A 441 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8228 (ttm) REVERT: A 1356 TRP cc_start: 0.8113 (p-90) cc_final: 0.7617 (p-90) REVERT: A 1357 LYS cc_start: 0.8199 (pttm) cc_final: 0.7989 (pptt) REVERT: A 1362 ASP cc_start: 0.7482 (m-30) cc_final: 0.7188 (t0) REVERT: A 1509 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7832 (pm20) REVERT: A 1516 GLU cc_start: 0.8532 (tp30) cc_final: 0.8296 (mp0) REVERT: A 1592 MET cc_start: 0.8079 (tpt) cc_final: 0.7694 (tpt) REVERT: A 1625 HIS cc_start: 0.7846 (m90) cc_final: 0.7504 (m90) REVERT: A 1626 TRP cc_start: 0.7165 (m100) cc_final: 0.6929 (m100) REVERT: A 1744 LYS cc_start: 0.8934 (ptpp) cc_final: 0.8644 (tppp) REVERT: A 1794 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7024 (mp10) REVERT: A 1829 TRP cc_start: 0.8572 (m100) cc_final: 0.8224 (m100) REVERT: A 1871 MET cc_start: 0.8160 (ptp) cc_final: 0.7723 (ptm) REVERT: A 1927 MET cc_start: 0.7660 (mtp) cc_final: 0.7194 (mpm) REVERT: A 1933 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7980 (mm) REVERT: A 1958 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7466 (mp0) REVERT: A 1993 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: A 2094 MET cc_start: 0.8397 (tpt) cc_final: 0.8016 (tpt) REVERT: A 2097 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8748 (mt) REVERT: A 2154 GLU cc_start: 0.8773 (pp20) cc_final: 0.8077 (tm-30) REVERT: A 2337 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8496 (pt) REVERT: A 2437 ASP cc_start: 0.8935 (m-30) cc_final: 0.8672 (m-30) REVERT: A 2800 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8428 (mtp180) REVERT: A 2860 ASP cc_start: 0.8678 (t70) cc_final: 0.8428 (t0) REVERT: A 3029 LYS cc_start: 0.8918 (mmmt) cc_final: 0.8602 (mttm) REVERT: A 3414 MET cc_start: 0.8688 (mmm) cc_final: 0.8451 (mmm) REVERT: A 3607 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8472 (pt0) REVERT: A 3609 MET cc_start: 0.8658 (mmt) cc_final: 0.8416 (mmp) REVERT: A 3613 MET cc_start: 0.8018 (tmt) cc_final: 0.7677 (tmt) REVERT: B 48 MET cc_start: 0.7171 (mmp) cc_final: 0.6872 (mmm) REVERT: B 121 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8311 (tp40) REVERT: B 212 ASP cc_start: 0.7966 (t0) cc_final: 0.7722 (t0) REVERT: C 20 MET cc_start: 0.4070 (OUTLIER) cc_final: 0.3633 (mpp) REVERT: C 40 MET cc_start: 0.7888 (ppp) cc_final: 0.7583 (ppp) REVERT: D 238 MET cc_start: 0.9005 (mtt) cc_final: 0.8607 (mtm) REVERT: D 267 TRP cc_start: 0.6915 (m-90) cc_final: 0.6597 (m-90) REVERT: D 348 MET cc_start: 0.8770 (tpp) cc_final: 0.8485 (tpp) outliers start: 97 outliers final: 28 residues processed: 352 average time/residue: 0.8067 time to fit residues: 350.0650 Evaluate side-chains 274 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1794 GLN Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3077 ILE Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3607 GLU Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3850 HIS Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 344 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 48 optimal weight: 0.7980 chunk 442 optimal weight: 20.0000 chunk 488 optimal weight: 0.9990 chunk 339 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 417 optimal weight: 0.0770 chunk 88 optimal weight: 0.0270 chunk 83 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 364 optimal weight: 3.9990 chunk 491 optimal weight: 20.0000 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN A 399 GLN A1725 GLN A2170 GLN A2787 HIS A2859 GLN A3501 HIS A3850 HIS C 119 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.101603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.067925 restraints weight = 276008.298| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 4.64 r_work: 0.2979 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 45778 Z= 0.111 Angle : 0.546 11.555 62145 Z= 0.275 Chirality : 0.039 0.408 6962 Planarity : 0.004 0.063 7706 Dihedral : 12.623 90.800 6622 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.45 % Allowed : 10.94 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % 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: 0.09 (0.12), residues: 5367 helix: 1.16 (0.10), residues: 3066 sheet: -0.93 (0.30), residues: 265 loop : -1.52 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3833 TYR 0.028 0.001 TYR A1873 PHE 0.025 0.001 PHE A2260 TRP 0.024 0.001 TRP D 267 HIS 0.014 0.001 HIS A3850 Details of bonding type rmsd covalent geometry : bond 0.00248 (45774) covalent geometry : angle 0.54498 (62143) hydrogen bonds : bond 0.03463 ( 2345) hydrogen bonds : angle 4.03353 ( 6765) metal coordination : bond 0.00476 ( 4) metal coordination : angle 4.87225 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 255 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4950 (tpp) cc_final: 0.4584 (tmm) REVERT: A 208 MET cc_start: 0.8467 (mtm) cc_final: 0.8073 (mtm) REVERT: A 247 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7855 (mp0) REVERT: A 326 MET cc_start: 0.8493 (mmm) cc_final: 0.8181 (mtt) REVERT: A 408 TYR cc_start: 0.8640 (m-80) cc_final: 0.8283 (m-80) REVERT: A 441 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8262 (ttm) REVERT: A 723 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7722 (p0) REVERT: A 858 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8961 (tpt) REVERT: A 1356 TRP cc_start: 0.8087 (p-90) cc_final: 0.7697 (p-90) REVERT: A 1357 LYS cc_start: 0.8128 (pttm) cc_final: 0.7919 (pptt) REVERT: A 1362 ASP cc_start: 0.7285 (m-30) cc_final: 0.6929 (t0) REVERT: A 1509 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7778 (pm20) REVERT: A 1592 MET cc_start: 0.8107 (tpt) cc_final: 0.7654 (tpt) REVERT: A 1625 HIS cc_start: 0.7888 (m90) cc_final: 0.7522 (m90) REVERT: A 1626 TRP cc_start: 0.7311 (m100) cc_final: 0.6772 (m100) REVERT: A 1744 LYS cc_start: 0.8996 (ptpp) cc_final: 0.8692 (tppp) REVERT: A 1829 TRP cc_start: 0.8565 (m100) cc_final: 0.8199 (m100) REVERT: A 1871 MET cc_start: 0.8205 (ptp) cc_final: 0.7783 (ptm) REVERT: A 1874 TYR cc_start: 0.8280 (m-80) cc_final: 0.8013 (m-80) REVERT: A 1927 MET cc_start: 0.7734 (mtp) cc_final: 0.7156 (mpm) REVERT: A 1933 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7968 (mm) REVERT: A 1958 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7500 (mp0) REVERT: A 1993 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: A 2094 MET cc_start: 0.8373 (tpt) cc_final: 0.8041 (tpt) REVERT: A 2199 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7584 (mm) REVERT: A 2281 MET cc_start: 0.9123 (tpp) cc_final: 0.8851 (mmp) REVERT: A 2437 ASP cc_start: 0.8960 (m-30) cc_final: 0.8701 (m-30) REVERT: A 2605 MET cc_start: 0.8958 (mtt) cc_final: 0.8735 (mtt) REVERT: A 2800 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8423 (mtp180) REVERT: A 2860 ASP cc_start: 0.8579 (t70) cc_final: 0.8342 (t0) REVERT: A 3029 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8670 (mptp) REVERT: A 3414 MET cc_start: 0.8593 (mmm) cc_final: 0.8336 (mmm) REVERT: A 3607 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8509 (pt0) REVERT: A 3609 MET cc_start: 0.8613 (mmt) cc_final: 0.8337 (mmp) REVERT: A 3613 MET cc_start: 0.8084 (tmt) cc_final: 0.7662 (tmt) REVERT: A 3796 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8277 (mtt) REVERT: B 48 MET cc_start: 0.7086 (mmp) cc_final: 0.6858 (mmm) REVERT: B 135 MET cc_start: 0.6463 (mtp) cc_final: 0.6255 (mtp) REVERT: B 212 ASP cc_start: 0.8052 (t0) cc_final: 0.7790 (t0) REVERT: C 20 MET cc_start: 0.3903 (OUTLIER) cc_final: 0.3501 (mpp) REVERT: C 40 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7532 (ppp) REVERT: C 84 MET cc_start: 0.7294 (mmp) cc_final: 0.6951 (mmm) REVERT: C 427 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7494 (ppp) REVERT: D 267 TRP cc_start: 0.7057 (m-90) cc_final: 0.6685 (m-90) REVERT: D 348 MET cc_start: 0.8772 (tpp) cc_final: 0.8407 (tpp) outliers start: 69 outliers final: 24 residues processed: 306 average time/residue: 0.7165 time to fit residues: 271.1112 Evaluate side-chains 267 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1688 LEU Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3607 GLU Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 344 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 435 optimal weight: 30.0000 chunk 505 optimal weight: 2.9990 chunk 492 optimal weight: 10.0000 chunk 395 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 385 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 511 optimal weight: 4.9990 chunk 423 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN A 399 GLN A2859 GLN A3643 HIS A3664 ASN B 68 GLN B 126 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.100312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066067 restraints weight = 291232.178| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.62 r_work: 0.2940 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 45778 Z= 0.152 Angle : 0.568 11.538 62145 Z= 0.287 Chirality : 0.041 0.374 6962 Planarity : 0.004 0.054 7706 Dihedral : 12.356 89.154 6615 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.82 % Allowed : 11.19 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % 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: 0.32 (0.12), residues: 5367 helix: 1.30 (0.10), residues: 3064 sheet: -0.73 (0.30), residues: 269 loop : -1.36 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 230 TYR 0.023 0.001 TYR A1873 PHE 0.026 0.002 PHE A2260 TRP 0.020 0.001 TRP D 267 HIS 0.008 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00361 (45774) covalent geometry : angle 0.56709 (62143) hydrogen bonds : bond 0.03707 ( 2345) hydrogen bonds : angle 3.97594 ( 6765) metal coordination : bond 0.00944 ( 4) metal coordination : angle 4.77594 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 242 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4855 (tpp) cc_final: 0.4348 (tmm) REVERT: A 326 MET cc_start: 0.8515 (mmm) cc_final: 0.8225 (mtt) REVERT: A 441 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8261 (ttm) REVERT: A 899 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8420 (ttp-170) REVERT: A 1356 TRP cc_start: 0.8110 (p-90) cc_final: 0.7642 (p-90) REVERT: A 1509 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7772 (pm20) REVERT: A 1592 MET cc_start: 0.8131 (tpt) cc_final: 0.7776 (tpt) REVERT: A 1626 TRP cc_start: 0.7347 (m100) cc_final: 0.7013 (m100) REVERT: A 1668 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6330 (m-80) REVERT: A 1744 LYS cc_start: 0.9008 (ptpp) cc_final: 0.8755 (tppp) REVERT: A 1774 MET cc_start: 0.8413 (tpp) cc_final: 0.8019 (tpp) REVERT: A 1794 GLN cc_start: 0.8103 (pm20) cc_final: 0.7707 (mp10) REVERT: A 1829 TRP cc_start: 0.8559 (m100) cc_final: 0.8156 (m100) REVERT: A 1871 MET cc_start: 0.8327 (ptp) cc_final: 0.7813 (ptm) REVERT: A 1874 TYR cc_start: 0.8223 (m-80) cc_final: 0.7973 (m-80) REVERT: A 1927 MET cc_start: 0.7739 (mtp) cc_final: 0.7220 (mpm) REVERT: A 1933 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7749 (mm) REVERT: A 1958 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7512 (mp0) REVERT: A 1993 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: A 2040 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8410 (mtp) REVERT: A 2094 MET cc_start: 0.8434 (tpt) cc_final: 0.8134 (tpt) REVERT: A 2437 ASP cc_start: 0.8958 (m-30) cc_final: 0.8701 (m-30) REVERT: A 2605 MET cc_start: 0.9031 (mtt) cc_final: 0.8769 (mtt) REVERT: A 2860 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8420 (t0) REVERT: A 3029 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8624 (mptp) REVERT: A 3607 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8569 (pt0) REVERT: A 3609 MET cc_start: 0.8620 (mmt) cc_final: 0.8348 (mmp) REVERT: A 3613 MET cc_start: 0.7924 (tmt) cc_final: 0.7520 (tmt) REVERT: A 3664 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8234 (p0) REVERT: A 3796 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8360 (mtt) REVERT: B 48 MET cc_start: 0.7237 (mmp) cc_final: 0.6999 (mmm) REVERT: B 212 ASP cc_start: 0.8017 (t0) cc_final: 0.7702 (t0) REVERT: C 20 MET cc_start: 0.3658 (OUTLIER) cc_final: 0.3236 (mpp) REVERT: C 40 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7605 (ppp) REVERT: C 346 CYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7455 (m) REVERT: C 427 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7596 (ppp) REVERT: D 1 MET cc_start: 0.7218 (tpp) cc_final: 0.5296 (mtt) REVERT: D 267 TRP cc_start: 0.7044 (m-90) cc_final: 0.6684 (m-90) REVERT: D 348 MET cc_start: 0.8806 (tpp) cc_final: 0.8484 (tpp) outliers start: 87 outliers final: 30 residues processed: 310 average time/residue: 0.7686 time to fit residues: 294.8460 Evaluate side-chains 272 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 899 ARG Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1981 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2040 MET Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2860 ASP Chi-restraints excluded: chain A residue 3038 GLU Chi-restraints excluded: chain A residue 3480 LEU Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3607 GLU Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 344 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 487 optimal weight: 5.9990 chunk 474 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 387 optimal weight: 4.9990 chunk 373 optimal weight: 6.9990 chunk 378 optimal weight: 0.7980 chunk 466 optimal weight: 10.0000 chunk 530 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 192 ASN A1691 GLN A1725 GLN A2859 GLN A3664 ASN B 174 ASN C 80 HIS C 622 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.100190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.066644 restraints weight = 287185.257| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 4.70 r_work: 0.2930 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 45778 Z= 0.147 Angle : 0.557 10.453 62145 Z= 0.281 Chirality : 0.041 0.363 6962 Planarity : 0.004 0.049 7706 Dihedral : 12.188 88.801 6612 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.76 % Allowed : 11.85 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % 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: 0.46 (0.12), residues: 5367 helix: 1.42 (0.10), residues: 3060 sheet: -0.58 (0.30), residues: 269 loop : -1.30 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 230 TYR 0.020 0.001 TYR A1873 PHE 0.032 0.001 PHE A3659 TRP 0.017 0.001 TRP A1632 HIS 0.007 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00350 (45774) covalent geometry : angle 0.55657 (62143) hydrogen bonds : bond 0.03554 ( 2345) hydrogen bonds : angle 3.94503 ( 6765) metal coordination : bond 0.00996 ( 4) metal coordination : angle 4.83076 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 237 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4983 (tpp) cc_final: 0.4455 (tmm) REVERT: A 326 MET cc_start: 0.8530 (mmm) cc_final: 0.8265 (mtt) REVERT: A 1356 TRP cc_start: 0.8114 (p-90) cc_final: 0.7796 (p-90) REVERT: A 1583 MET cc_start: 0.7600 (mmm) cc_final: 0.7187 (pp-130) REVERT: A 1592 MET cc_start: 0.8081 (tpt) cc_final: 0.7762 (tpt) REVERT: A 1626 TRP cc_start: 0.7362 (m100) cc_final: 0.6985 (m100) REVERT: A 1668 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.5915 (t80) REVERT: A 1744 LYS cc_start: 0.9004 (ptpp) cc_final: 0.8747 (tppp) REVERT: A 1829 TRP cc_start: 0.8587 (m100) cc_final: 0.8197 (m100) REVERT: A 1871 MET cc_start: 0.8368 (ptp) cc_final: 0.7837 (ptm) REVERT: A 1881 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: A 1927 MET cc_start: 0.7592 (mtp) cc_final: 0.7186 (mpm) REVERT: A 1933 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7781 (mm) REVERT: A 1958 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7510 (mp0) REVERT: A 1993 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: A 2094 MET cc_start: 0.8437 (tpt) cc_final: 0.8138 (tpt) REVERT: A 2437 ASP cc_start: 0.8968 (m-30) cc_final: 0.8704 (m-30) REVERT: A 2605 MET cc_start: 0.9013 (mtt) cc_final: 0.8738 (mtt) REVERT: A 2800 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8492 (mtp180) REVERT: A 2860 ASP cc_start: 0.8679 (t70) cc_final: 0.8437 (t0) REVERT: A 3029 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8603 (mptp) REVERT: A 3606 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7981 (mm) REVERT: A 3607 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8525 (pt0) REVERT: A 3609 MET cc_start: 0.8647 (mmt) cc_final: 0.8378 (mmp) REVERT: A 3613 MET cc_start: 0.8057 (tmt) cc_final: 0.7599 (tmt) REVERT: A 3796 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8385 (mtt) REVERT: B 48 MET cc_start: 0.7324 (mmp) cc_final: 0.7051 (mmm) REVERT: B 212 ASP cc_start: 0.7882 (t0) cc_final: 0.7551 (t0) REVERT: B 290 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7739 (ttm110) REVERT: C 20 MET cc_start: 0.3783 (OUTLIER) cc_final: 0.3330 (mpp) REVERT: C 40 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7676 (ppp) REVERT: C 346 CYS cc_start: 0.7936 (p) cc_final: 0.7501 (m) REVERT: C 427 MET cc_start: 0.7954 (ptt) cc_final: 0.7719 (ppp) REVERT: D 267 TRP cc_start: 0.6984 (m-90) cc_final: 0.6663 (m-90) REVERT: D 348 MET cc_start: 0.8806 (tpp) cc_final: 0.8451 (tpp) outliers start: 84 outliers final: 33 residues processed: 300 average time/residue: 0.6832 time to fit residues: 255.0146 Evaluate side-chains 271 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1423 ILE Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1881 TYR Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 3173 MET Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3606 ILE Chi-restraints excluded: chain A residue 3607 GLU Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 520 optimal weight: 0.8980 chunk 280 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 534 optimal weight: 10.0000 chunk 363 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 168 optimal weight: 30.0000 chunk 532 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 412 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1725 GLN A3319 ASN ** A3397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.099346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.064443 restraints weight = 267748.570| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.35 r_work: 0.2914 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 45778 Z= 0.182 Angle : 0.588 11.557 62145 Z= 0.296 Chirality : 0.042 0.353 6962 Planarity : 0.004 0.045 7706 Dihedral : 12.135 86.366 6610 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.86 % Allowed : 12.14 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % 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: 0.51 (0.12), residues: 5367 helix: 1.41 (0.10), residues: 3059 sheet: -0.52 (0.31), residues: 267 loop : -1.21 (0.14), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 230 TYR 0.019 0.001 TYR A1873 PHE 0.027 0.002 PHE A1814 TRP 0.021 0.001 TRP A1632 HIS 0.010 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00435 (45774) covalent geometry : angle 0.58739 (62143) hydrogen bonds : bond 0.03869 ( 2345) hydrogen bonds : angle 4.00118 ( 6765) metal coordination : bond 0.01562 ( 4) metal coordination : angle 5.08688 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 236 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4871 (tpp) cc_final: 0.4266 (tmm) REVERT: A 286 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7193 (pp) REVERT: A 326 MET cc_start: 0.8555 (mmm) cc_final: 0.8328 (mtt) REVERT: A 899 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8609 (ttp-170) REVERT: A 1197 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8587 (pp) REVERT: A 1356 TRP cc_start: 0.8164 (p-90) cc_final: 0.7709 (p-90) REVERT: A 1583 MET cc_start: 0.7571 (mmm) cc_final: 0.7307 (pp-130) REVERT: A 1592 MET cc_start: 0.8131 (tpt) cc_final: 0.7845 (tpt) REVERT: A 1626 TRP cc_start: 0.7392 (m100) cc_final: 0.7027 (m100) REVERT: A 1668 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.5871 (t80) REVERT: A 1774 MET cc_start: 0.8352 (tpp) cc_final: 0.8067 (tpp) REVERT: A 1794 GLN cc_start: 0.7998 (pm20) cc_final: 0.7278 (mp10) REVERT: A 1829 TRP cc_start: 0.8575 (m100) cc_final: 0.8292 (m100) REVERT: A 1871 MET cc_start: 0.8412 (ptp) cc_final: 0.7908 (ptm) REVERT: A 1881 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.7621 (m-80) REVERT: A 1927 MET cc_start: 0.7536 (mtp) cc_final: 0.7041 (mmt) REVERT: A 1933 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7808 (mm) REVERT: A 1958 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7535 (mp0) REVERT: A 1993 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: A 2094 MET cc_start: 0.8454 (tpt) cc_final: 0.8230 (tpt) REVERT: A 2357 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8195 (pt0) REVERT: A 2437 ASP cc_start: 0.8981 (m-30) cc_final: 0.8708 (m-30) REVERT: A 2800 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8514 (mtp180) REVERT: A 2860 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8454 (t0) REVERT: A 3029 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8592 (mptp) REVERT: A 3607 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8493 (pt0) REVERT: A 3609 MET cc_start: 0.8639 (mmt) cc_final: 0.8376 (mmp) REVERT: A 3654 MET cc_start: 0.7189 (tpt) cc_final: 0.6718 (tmt) REVERT: A 3796 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8434 (mtt) REVERT: B 48 MET cc_start: 0.7502 (mmp) cc_final: 0.7247 (mmm) REVERT: B 71 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.6483 (t80) REVERT: B 212 ASP cc_start: 0.7903 (t0) cc_final: 0.7585 (t0) REVERT: B 290 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7739 (ttm110) REVERT: C 20 MET cc_start: 0.3694 (OUTLIER) cc_final: 0.3217 (mpp) REVERT: C 40 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7622 (ppp) REVERT: C 212 MET cc_start: 0.4305 (tpt) cc_final: 0.3963 (tpt) REVERT: C 346 CYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7542 (m) REVERT: C 427 MET cc_start: 0.8055 (ptt) cc_final: 0.7805 (ppp) REVERT: C 632 PHE cc_start: 0.7076 (m-10) cc_final: 0.6643 (m-10) REVERT: D 267 TRP cc_start: 0.7020 (m-10) cc_final: 0.6711 (m-90) REVERT: D 348 MET cc_start: 0.8837 (tpp) cc_final: 0.8486 (tpp) REVERT: D 397 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7771 (tm) outliers start: 89 outliers final: 33 residues processed: 304 average time/residue: 0.7393 time to fit residues: 280.4643 Evaluate side-chains 277 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 899 ARG Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1423 ILE Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1881 TYR Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2357 GLU Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 2860 ASP Chi-restraints excluded: chain A residue 3173 MET Chi-restraints excluded: chain A residue 3480 LEU Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3607 GLU Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4029 GLN Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 143 optimal weight: 0.0970 chunk 281 optimal weight: 2.9990 chunk 121 optimal weight: 0.0010 chunk 435 optimal weight: 30.0000 chunk 303 optimal weight: 0.0570 chunk 23 optimal weight: 9.9990 chunk 523 optimal weight: 0.1980 chunk 264 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 359 optimal weight: 0.9980 overall best weight: 0.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A1687 HIS A1691 GLN A2859 GLN A3384 HIS ** A3397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.101150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.069129 restraints weight = 240466.837| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.61 r_work: 0.2942 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 45778 Z= 0.104 Angle : 0.545 18.236 62145 Z= 0.271 Chirality : 0.039 0.350 6962 Planarity : 0.004 0.061 7706 Dihedral : 11.844 86.474 6608 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.49 % Allowed : 12.70 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % 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: 0.76 (0.12), residues: 5367 helix: 1.63 (0.10), residues: 3066 sheet: -0.42 (0.31), residues: 269 loop : -1.13 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 142 TYR 0.020 0.001 TYR A1873 PHE 0.026 0.001 PHE A2260 TRP 0.018 0.001 TRP A1632 HIS 0.003 0.000 HIS A1625 Details of bonding type rmsd covalent geometry : bond 0.00227 (45774) covalent geometry : angle 0.54396 (62143) hydrogen bonds : bond 0.03087 ( 2345) hydrogen bonds : angle 3.87948 ( 6765) metal coordination : bond 0.00398 ( 4) metal coordination : angle 4.66531 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 236 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4871 (tpp) cc_final: 0.4248 (tmm) REVERT: A 326 MET cc_start: 0.8538 (mmm) cc_final: 0.8312 (mtt) REVERT: A 399 GLN cc_start: 0.5399 (OUTLIER) cc_final: 0.5084 (pp30) REVERT: A 899 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8578 (ttp-170) REVERT: A 1356 TRP cc_start: 0.8126 (p-90) cc_final: 0.7795 (p-90) REVERT: A 1583 MET cc_start: 0.7600 (mmm) cc_final: 0.7256 (ppp) REVERT: A 1592 MET cc_start: 0.8091 (tpt) cc_final: 0.7794 (tpt) REVERT: A 1626 TRP cc_start: 0.7214 (m100) cc_final: 0.6743 (m100) REVERT: A 1688 LEU cc_start: 0.8629 (pp) cc_final: 0.8359 (tp) REVERT: A 1774 MET cc_start: 0.8348 (tpp) cc_final: 0.8095 (tpp) REVERT: A 1794 GLN cc_start: 0.8020 (pm20) cc_final: 0.7119 (mp10) REVERT: A 1829 TRP cc_start: 0.8615 (m100) cc_final: 0.8236 (m100) REVERT: A 1871 MET cc_start: 0.8304 (ptp) cc_final: 0.7753 (ptm) REVERT: A 1927 MET cc_start: 0.7556 (mtp) cc_final: 0.7154 (mpm) REVERT: A 1933 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7805 (mm) REVERT: A 1993 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: A 2094 MET cc_start: 0.8419 (tpt) cc_final: 0.8149 (tpt) REVERT: A 2289 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7915 (t0) REVERT: A 2331 MET cc_start: 0.8244 (tpp) cc_final: 0.7687 (tpt) REVERT: A 2437 ASP cc_start: 0.9020 (m-30) cc_final: 0.8775 (m-30) REVERT: A 2800 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8505 (mtp180) REVERT: A 2860 ASP cc_start: 0.8608 (t70) cc_final: 0.8375 (t0) REVERT: A 3029 LYS cc_start: 0.8959 (mmmt) cc_final: 0.8611 (mptp) REVERT: A 3607 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: A 3609 MET cc_start: 0.8616 (mmt) cc_final: 0.8341 (mmp) REVERT: A 3613 MET cc_start: 0.8071 (tmt) cc_final: 0.7641 (tmt) REVERT: B 48 MET cc_start: 0.7354 (mmp) cc_final: 0.7134 (mmm) REVERT: B 212 ASP cc_start: 0.7871 (t0) cc_final: 0.7590 (t0) REVERT: B 290 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7860 (ttm110) REVERT: C 20 MET cc_start: 0.3821 (OUTLIER) cc_final: 0.3313 (mpp) REVERT: C 40 MET cc_start: 0.8006 (ppp) cc_final: 0.7729 (ppp) REVERT: C 212 MET cc_start: 0.4383 (tpt) cc_final: 0.3992 (tpt) REVERT: C 346 CYS cc_start: 0.7983 (p) cc_final: 0.7508 (m) REVERT: C 632 PHE cc_start: 0.7111 (m-10) cc_final: 0.6696 (m-10) REVERT: D 267 TRP cc_start: 0.6964 (m-10) cc_final: 0.6687 (m-90) REVERT: D 348 MET cc_start: 0.8820 (tpp) cc_final: 0.8532 (tpp) REVERT: D 397 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7706 (tm) outliers start: 71 outliers final: 29 residues processed: 293 average time/residue: 0.5381 time to fit residues: 196.4006 Evaluate side-chains 262 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 899 ARG Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2289 ASP Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2473 MET Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3607 GLU Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 70 optimal weight: 2.9990 chunk 448 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 391 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 490 optimal weight: 20.0000 chunk 475 optimal weight: 20.0000 chunk 364 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A1890 HIS A1897 ASN A2859 GLN A2977 ASN ** A3397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS B 515 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.098214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.064630 restraints weight = 293235.044| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 4.76 r_work: 0.2865 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 45778 Z= 0.280 Angle : 0.669 16.531 62145 Z= 0.338 Chirality : 0.045 0.338 6962 Planarity : 0.005 0.055 7706 Dihedral : 12.126 85.349 6607 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.74 % Allowed : 12.64 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % 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: 0.43 (0.12), residues: 5367 helix: 1.31 (0.10), residues: 3049 sheet: -0.63 (0.30), residues: 276 loop : -1.14 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 230 TYR 0.024 0.002 TYR A1107 PHE 0.029 0.002 PHE A2260 TRP 0.021 0.002 TRP A1039 HIS 0.014 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00664 (45774) covalent geometry : angle 0.66855 (62143) hydrogen bonds : bond 0.04560 ( 2345) hydrogen bonds : angle 4.15491 ( 6765) metal coordination : bond 0.02524 ( 4) metal coordination : angle 5.28097 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 230 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4813 (tpp) cc_final: 0.4207 (tmm) REVERT: A 286 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7241 (pp) REVERT: A 399 GLN cc_start: 0.5593 (OUTLIER) cc_final: 0.5170 (pp30) REVERT: A 723 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8141 (p0) REVERT: A 1356 TRP cc_start: 0.8139 (p-90) cc_final: 0.7611 (p-90) REVERT: A 1583 MET cc_start: 0.7534 (mmm) cc_final: 0.7254 (ppp) REVERT: A 1592 MET cc_start: 0.8188 (tpt) cc_final: 0.7941 (tpt) REVERT: A 1626 TRP cc_start: 0.7208 (m100) cc_final: 0.6917 (m100) REVERT: A 1688 LEU cc_start: 0.8681 (pp) cc_final: 0.8454 (tp) REVERT: A 1774 MET cc_start: 0.8442 (tpp) cc_final: 0.8110 (tpp) REVERT: A 1794 GLN cc_start: 0.8044 (pm20) cc_final: 0.7181 (mp10) REVERT: A 1829 TRP cc_start: 0.8565 (m100) cc_final: 0.8227 (m100) REVERT: A 1871 MET cc_start: 0.8432 (ptp) cc_final: 0.7949 (ptm) REVERT: A 1927 MET cc_start: 0.7543 (mtp) cc_final: 0.7034 (mmt) REVERT: A 1933 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7837 (mm) REVERT: A 1993 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: A 2289 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7903 (t0) REVERT: A 2437 ASP cc_start: 0.9048 (m-30) cc_final: 0.8779 (m-30) REVERT: A 2605 MET cc_start: 0.9058 (mtt) cc_final: 0.8792 (mtt) REVERT: A 2800 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8550 (mtp180) REVERT: A 2860 ASP cc_start: 0.8815 (t70) cc_final: 0.8588 (t0) REVERT: A 3029 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8614 (mptp) REVERT: A 3242 MET cc_start: 0.9088 (ttt) cc_final: 0.8887 (ttt) REVERT: A 3609 MET cc_start: 0.8631 (mmt) cc_final: 0.8376 (mmp) REVERT: A 3613 MET cc_start: 0.8078 (tmt) cc_final: 0.7696 (tmt) REVERT: B 48 MET cc_start: 0.7523 (mmp) cc_final: 0.7164 (mmm) REVERT: B 290 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7671 (ttm110) REVERT: C 20 MET cc_start: 0.3499 (OUTLIER) cc_final: 0.3149 (mpp) REVERT: C 40 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7566 (ppp) REVERT: C 212 MET cc_start: 0.4497 (tpt) cc_final: 0.4182 (tpt) REVERT: C 346 CYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7538 (m) REVERT: C 632 PHE cc_start: 0.7094 (m-10) cc_final: 0.6718 (m-10) REVERT: D 267 TRP cc_start: 0.7004 (m-10) cc_final: 0.6692 (m-90) REVERT: D 348 MET cc_start: 0.8857 (tpp) cc_final: 0.8506 (tpp) REVERT: D 397 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7781 (tm) outliers start: 83 outliers final: 41 residues processed: 295 average time/residue: 0.4669 time to fit residues: 172.7370 Evaluate side-chains 279 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1423 ILE Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2185 MET Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2281 MET Chi-restraints excluded: chain A residue 2289 ASP Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2473 MET Chi-restraints excluded: chain A residue 2631 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 3480 LEU Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4029 GLN Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 128 optimal weight: 0.8980 chunk 225 optimal weight: 0.7980 chunk 401 optimal weight: 7.9990 chunk 389 optimal weight: 0.0770 chunk 261 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 168 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 403 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1890 HIS A2859 GLN ** A3397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.100548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.067480 restraints weight = 281818.085| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.87 r_work: 0.2928 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 45778 Z= 0.110 Angle : 0.565 16.987 62145 Z= 0.281 Chirality : 0.040 0.340 6962 Planarity : 0.004 0.055 7706 Dihedral : 11.814 86.151 6604 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.22 % Allowed : 13.22 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % 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: 0.75 (0.12), residues: 5367 helix: 1.56 (0.10), residues: 3067 sheet: -0.33 (0.31), residues: 269 loop : -1.05 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 230 TYR 0.020 0.001 TYR A1873 PHE 0.025 0.001 PHE A2260 TRP 0.016 0.001 TRP A1632 HIS 0.004 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00247 (45774) covalent geometry : angle 0.56400 (62143) hydrogen bonds : bond 0.03269 ( 2345) hydrogen bonds : angle 3.92401 ( 6765) metal coordination : bond 0.00540 ( 4) metal coordination : angle 4.94194 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 228 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4829 (tpp) cc_final: 0.4187 (tmm) REVERT: A 286 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7200 (pp) REVERT: A 326 MET cc_start: 0.8518 (mmm) cc_final: 0.8207 (mtt) REVERT: A 1356 TRP cc_start: 0.8177 (p-90) cc_final: 0.7665 (p-90) REVERT: A 1583 MET cc_start: 0.7550 (mmm) cc_final: 0.7260 (ppp) REVERT: A 1592 MET cc_start: 0.8163 (tpt) cc_final: 0.7894 (tpt) REVERT: A 1626 TRP cc_start: 0.7157 (m100) cc_final: 0.6749 (m100) REVERT: A 1688 LEU cc_start: 0.8690 (pp) cc_final: 0.8458 (tp) REVERT: A 1774 MET cc_start: 0.8405 (tpp) cc_final: 0.8093 (tpp) REVERT: A 1794 GLN cc_start: 0.8063 (pm20) cc_final: 0.7219 (mp10) REVERT: A 1829 TRP cc_start: 0.8626 (m100) cc_final: 0.8247 (m100) REVERT: A 1871 MET cc_start: 0.8293 (ptp) cc_final: 0.7792 (ptm) REVERT: A 1880 MET cc_start: 0.9139 (ptp) cc_final: 0.8453 (tmt) REVERT: A 1881 TYR cc_start: 0.8773 (m-80) cc_final: 0.8049 (t80) REVERT: A 1927 MET cc_start: 0.7504 (mtp) cc_final: 0.6995 (mmt) REVERT: A 1933 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7832 (mm) REVERT: A 1993 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: A 2289 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7866 (t0) REVERT: A 2331 MET cc_start: 0.8213 (tpp) cc_final: 0.7703 (tpt) REVERT: A 2437 ASP cc_start: 0.9007 (m-30) cc_final: 0.8755 (m-30) REVERT: A 2800 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8485 (mtp180) REVERT: A 2860 ASP cc_start: 0.8640 (t70) cc_final: 0.8404 (t0) REVERT: A 3029 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8612 (mptp) REVERT: A 3609 MET cc_start: 0.8591 (mmt) cc_final: 0.8338 (mmp) REVERT: A 3613 MET cc_start: 0.8019 (tmt) cc_final: 0.7554 (tmt) REVERT: B 48 MET cc_start: 0.7388 (mmp) cc_final: 0.7082 (mmm) REVERT: B 212 ASP cc_start: 0.7835 (t0) cc_final: 0.7574 (t0) REVERT: B 290 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7745 (ttm110) REVERT: C 20 MET cc_start: 0.3618 (OUTLIER) cc_final: 0.3190 (mpp) REVERT: C 40 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7661 (ppp) REVERT: C 84 MET cc_start: 0.6994 (mmm) cc_final: 0.6774 (mmt) REVERT: C 346 CYS cc_start: 0.7980 (p) cc_final: 0.7532 (m) REVERT: C 632 PHE cc_start: 0.7154 (m-10) cc_final: 0.6894 (m-80) REVERT: D 1 MET cc_start: 0.7116 (tpp) cc_final: 0.6647 (tpt) REVERT: D 267 TRP cc_start: 0.7008 (m-10) cc_final: 0.6717 (m-90) REVERT: D 348 MET cc_start: 0.8824 (tpp) cc_final: 0.8467 (tpp) REVERT: D 397 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7755 (tm) outliers start: 58 outliers final: 31 residues processed: 274 average time/residue: 0.4796 time to fit residues: 165.6739 Evaluate side-chains 262 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2289 ASP Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 276 optimal weight: 0.6980 chunk 435 optimal weight: 30.0000 chunk 231 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 370 optimal weight: 2.9990 chunk 330 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 447 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A2859 GLN ** A3397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.099974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.067255 restraints weight = 236813.770| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 4.43 r_work: 0.2908 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 45778 Z= 0.136 Angle : 0.572 16.307 62145 Z= 0.285 Chirality : 0.040 0.335 6962 Planarity : 0.004 0.053 7706 Dihedral : 11.760 85.544 6604 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.08 % Allowed : 13.53 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % 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: 0.78 (0.12), residues: 5367 helix: 1.59 (0.10), residues: 3064 sheet: -0.44 (0.30), residues: 281 loop : -1.03 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 230 TYR 0.020 0.001 TYR A1873 PHE 0.025 0.001 PHE A2260 TRP 0.018 0.001 TRP A1632 HIS 0.006 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00322 (45774) covalent geometry : angle 0.57131 (62143) hydrogen bonds : bond 0.03451 ( 2345) hydrogen bonds : angle 3.91554 ( 6765) metal coordination : bond 0.01019 ( 4) metal coordination : angle 4.74014 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4753 (tpp) cc_final: 0.4118 (tmm) REVERT: A 286 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7244 (pp) REVERT: A 326 MET cc_start: 0.8504 (mmm) cc_final: 0.8196 (mtt) REVERT: A 1356 TRP cc_start: 0.8208 (p-90) cc_final: 0.7725 (p-90) REVERT: A 1583 MET cc_start: 0.7543 (mmm) cc_final: 0.7272 (ppp) REVERT: A 1592 MET cc_start: 0.8142 (tpt) cc_final: 0.7880 (tpt) REVERT: A 1626 TRP cc_start: 0.7076 (m100) cc_final: 0.6659 (m100) REVERT: A 1643 MET cc_start: 0.8711 (tmm) cc_final: 0.8419 (ptp) REVERT: A 1774 MET cc_start: 0.8445 (tpp) cc_final: 0.8058 (tpp) REVERT: A 1794 GLN cc_start: 0.8069 (pm20) cc_final: 0.7235 (mp10) REVERT: A 1829 TRP cc_start: 0.8599 (m100) cc_final: 0.8263 (m100) REVERT: A 1871 MET cc_start: 0.8383 (ptp) cc_final: 0.7827 (ptm) REVERT: A 1874 TYR cc_start: 0.8195 (m-80) cc_final: 0.7975 (m-80) REVERT: A 1880 MET cc_start: 0.9128 (ptp) cc_final: 0.8498 (tmt) REVERT: A 1881 TYR cc_start: 0.8784 (m-80) cc_final: 0.8056 (t80) REVERT: A 1927 MET cc_start: 0.7530 (mtp) cc_final: 0.7027 (mmt) REVERT: A 1933 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7817 (mm) REVERT: A 1993 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: A 2289 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7848 (t0) REVERT: A 2331 MET cc_start: 0.8283 (tpp) cc_final: 0.7748 (tpt) REVERT: A 2437 ASP cc_start: 0.9025 (m-30) cc_final: 0.8765 (m-30) REVERT: A 2605 MET cc_start: 0.9028 (mtt) cc_final: 0.8711 (mtt) REVERT: A 2800 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8488 (mtp180) REVERT: A 2860 ASP cc_start: 0.8708 (t70) cc_final: 0.8479 (t0) REVERT: A 3029 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8612 (mptp) REVERT: A 3609 MET cc_start: 0.8601 (mmt) cc_final: 0.8345 (mmp) REVERT: A 3613 MET cc_start: 0.8043 (tmt) cc_final: 0.7679 (tmt) REVERT: B 48 MET cc_start: 0.7414 (mmp) cc_final: 0.7092 (mmm) REVERT: B 212 ASP cc_start: 0.7838 (t0) cc_final: 0.7558 (t0) REVERT: B 290 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7740 (ttm110) REVERT: C 16 VAL cc_start: 0.4018 (OUTLIER) cc_final: 0.3714 (t) REVERT: C 20 MET cc_start: 0.3559 (OUTLIER) cc_final: 0.3132 (mpp) REVERT: C 40 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7643 (ppp) REVERT: C 84 MET cc_start: 0.6950 (mmm) cc_final: 0.6750 (mmt) REVERT: C 346 CYS cc_start: 0.7965 (p) cc_final: 0.7536 (m) REVERT: C 632 PHE cc_start: 0.7171 (m-10) cc_final: 0.6921 (m-80) REVERT: D 1 MET cc_start: 0.7110 (tpp) cc_final: 0.6634 (tpt) REVERT: D 267 TRP cc_start: 0.7024 (m-10) cc_final: 0.6719 (m-90) REVERT: D 348 MET cc_start: 0.8850 (tpp) cc_final: 0.8501 (tpp) REVERT: D 397 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7759 (tm) outliers start: 51 outliers final: 31 residues processed: 268 average time/residue: 0.4703 time to fit residues: 157.5899 Evaluate side-chains 264 residues out of total 4826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1981 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2185 MET Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2289 ASP Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 51 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 chunk 158 optimal weight: 0.0370 chunk 419 optimal weight: 0.9980 chunk 527 optimal weight: 0.6980 chunk 495 optimal weight: 10.0000 chunk 422 optimal weight: 0.0370 chunk 201 optimal weight: 2.9990 chunk 218 optimal weight: 0.4980 chunk 310 optimal weight: 5.9990 chunk 327 optimal weight: 3.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2859 GLN ** A3397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.101220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068406 restraints weight = 309064.234| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 5.02 r_work: 0.2957 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 45778 Z= 0.103 Angle : 0.557 16.819 62145 Z= 0.276 Chirality : 0.039 0.331 6962 Planarity : 0.004 0.054 7706 Dihedral : 11.558 85.429 6601 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.05 % Allowed : 13.51 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % 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: 0.92 (0.12), residues: 5367 helix: 1.70 (0.10), residues: 3070 sheet: -0.34 (0.30), residues: 282 loop : -0.97 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 230 TYR 0.022 0.001 TYR A1945 PHE 0.025 0.001 PHE A2260 TRP 0.017 0.001 TRP A1632 HIS 0.003 0.000 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00230 (45774) covalent geometry : angle 0.55607 (62143) hydrogen bonds : bond 0.03009 ( 2345) hydrogen bonds : angle 3.83042 ( 6765) metal coordination : bond 0.00396 ( 4) metal coordination : angle 4.22632 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14998.49 seconds wall clock time: 255 minutes 35.83 seconds (15335.83 seconds total)