Starting phenix.real_space_refine on Sat Sep 12 20:17:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v93_21115/09_2026/6v93_21115.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v93_21115/09_2026/6v93_21115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6v93_21115/09_2026/6v93_21115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v93_21115/09_2026/6v93_21115.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6v93_21115/09_2026/6v93_21115.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v93_21115/09_2026/6v93_21115.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v93_21115/09_2026/6v93_21115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v93_21115/09_2026/6v93_21115.map" } resolution = 3.1 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= 0.003 sd= 1.103 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 Ca 2 9.91 5 Fe 4 7.16 5 P 29 5.49 5 S 82 5.16 5 C 11534 2.51 5 N 2981 2.21 5 O 3473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "A PHE 598": not complete - not flipped Time to flip 79 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18105 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 9897 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1259, 9882 Classifications: {'peptide': 1259} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 74} Link IDs: {'PTRANS': 60, 'TRANS': 1198} Chain breaks: 8 Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 18, 'GLU:plan': 35, 'GLN:plan1': 11, 'ASN:plan1': 6, 'ARG:plan': 8, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 258 Conformer: "B" Number of residues, atoms: 1259, 9882 Classifications: {'peptide': 1259} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 74} Link IDs: {'PTRANS': 60, 'TRANS': 1198} Chain breaks: 8 Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 18, 'GLU:plan': 35, 'GLN:plan1': 11, 'ASN:plan1': 6, 'ARG:plan': 8, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 258 bond proxies already assigned to first conformer: 10100 Chain: "D" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1286 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1660 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3541 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 26, 'TRANS': 434} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 2, 'GLU:plan': 13, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 116 Chain: "G" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 929 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 212 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 322 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 175 Unusual residues: {' CA': 2, 'DCP': 1, 'SF4': 1} Classifications: {'undetermined': 4, 'water': 137} Link IDs: {None: 140} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9684 SG CYS A1473 60.219 72.205 67.257 1.00 42.97 S ATOM 9499 SG CYS A1449 54.514 69.839 65.125 1.00 44.24 S ATOM 9644 SG CYS A1468 57.621 66.825 70.044 1.00 41.77 S ATOM 9475 SG CYS A1446 55.075 72.427 71.345 1.00 45.69 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN A1259 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A1259 " occ=0.50 Time building chain proxies: 5.45, per 1000 atoms: 0.30 Number of scatterers: 18105 At special positions: 0 Unit cell: (134.156, 154.548, 115.911, 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) Fe 4 26.01 Ca 2 19.99 S 82 16.00 P 29 15.00 O 3473 8.00 N 2981 7.00 C 11534 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: 1.32 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1601 " pdb="FE3 SF4 A1601 " - pdb=" SG CYS A1468 " pdb="FE1 SF4 A1601 " - pdb=" SG CYS A1473 " pdb="FE2 SF4 A1601 " - pdb=" SG CYS A1449 " pdb="FE4 SF4 A1601 " - pdb=" SG CYS A1446 " Number of angles added : 12 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 22 sheets defined 37.9% alpha, 13.2% beta 10 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 95 through 116 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.110A pdb=" N LEU A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 233 " --> pdb=" O ILE A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 233' Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 307 through 322 removed outlier: 4.299A pdb=" N ASP A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 531 through 540 removed outlier: 4.207A pdb=" N ASN A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.537A pdb=" N LEU A 558 " --> pdb=" O PRO A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.550A pdb=" N LYS A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 735 Processing helix chain 'A' and resid 744 through 760 removed outlier: 3.565A pdb=" N MET A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.627A pdb=" N ALA A 794 " --> pdb=" O VAL A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 813 removed outlier: 3.613A pdb=" N TYR A 810 " --> pdb=" O ASP A 806 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 811 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 857 through 866 Processing helix chain 'A' and resid 870 through 895 removed outlier: 3.628A pdb=" N LEU A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 889 " --> pdb=" O ALA A 885 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 892 " --> pdb=" O ASN A 888 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 909 Processing helix chain 'A' and resid 912 through 916 removed outlier: 3.568A pdb=" N VAL A 915 " --> pdb=" O PHE A 912 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 916 " --> pdb=" O HIS A 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 916' Processing helix chain 'A' and resid 920 through 934 removed outlier: 3.616A pdb=" N VAL A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 949 removed outlier: 3.566A pdb=" N LYS A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 987 Processing helix chain 'A' and resid 1019 through 1024 Processing helix chain 'A' and resid 1044 through 1065 removed outlier: 4.044A pdb=" N LYS A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1095 removed outlier: 3.687A pdb=" N LYS A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A1077 " --> pdb=" O THR A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1129 Processing helix chain 'A' and resid 1157 through 1171 Processing helix chain 'A' and resid 1224 through 1242 removed outlier: 3.589A pdb=" N GLN A1228 " --> pdb=" O ILE A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1261 removed outlier: 3.766A pdb=" N ILE A1247 " --> pdb=" O ASP A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1299 removed outlier: 3.681A pdb=" N VAL A1290 " --> pdb=" O PRO A1286 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A1291 " --> pdb=" O ALA A1287 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU A1298 " --> pdb=" O ARG A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1327 removed outlier: 3.854A pdb=" N ARG A1326 " --> pdb=" O LEU A1322 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS A1327 " --> pdb=" O LEU A1323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1322 through 1327' Processing helix chain 'A' and resid 1329 through 1336 Processing helix chain 'A' and resid 1342 through 1361 Proline residue: A1353 - end of helix Processing helix chain 'A' and resid 1366 through 1372 removed outlier: 3.655A pdb=" N ALA A1370 " --> pdb=" O VAL A1366 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A1371 " --> pdb=" O GLY A1367 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A1372 " --> pdb=" O ASN A1368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1366 through 1372' Processing helix chain 'A' and resid 1423 through 1450 Processing helix chain 'A' and resid 1450 through 1455 Processing helix chain 'A' and resid 1460 through 1466 Processing helix chain 'A' and resid 1473 through 1487 removed outlier: 4.002A pdb=" N TYR A1477 " --> pdb=" O CYS A1473 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 24 removed outlier: 3.870A pdb=" N GLU D 6 " --> pdb=" O ASN D 2 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 68 removed outlier: 3.677A pdb=" N LYS D 68 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'E' and resid 4 through 24 removed outlier: 3.521A pdb=" N ARG E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 51 through 69 removed outlier: 3.555A pdb=" N ASP E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.676A pdb=" N VAL E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 175 Processing helix chain 'F' and resid 0 through 10 removed outlier: 3.724A pdb=" N GLU F 10 " --> pdb=" O THR F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 76 removed outlier: 3.885A pdb=" N ILE F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 125 Processing helix chain 'F' and resid 132 through 138 removed outlier: 4.029A pdb=" N TYR F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 241 removed outlier: 3.848A pdb=" N LEU F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 252 Processing helix chain 'F' and resid 272 through 291 removed outlier: 3.918A pdb=" N LEU F 276 " --> pdb=" O ASN F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 325 Processing helix chain 'F' and resid 357 through 364 Processing helix chain 'F' and resid 391 through 405 Processing helix chain 'F' and resid 411 through 416 Processing helix chain 'G' and resid 3 through 15 Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 32 through 45 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 35 removed outlier: 8.155A pdb=" N ILE A 268 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 72 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE A 270 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS A 74 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 163 removed outlier: 7.551A pdb=" N ILE A 938 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE A 146 " --> pdb=" O ILE A 938 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 189 removed outlier: 4.433A pdb=" N ILE A 188 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 521 through 522 removed outlier: 3.630A pdb=" N ARG D 74 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN D 81 " --> pdb=" O CYS D 87 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N CYS D 87 " --> pdb=" O ASN D 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 581 through 582 removed outlier: 6.496A pdb=" N ILE A 581 " --> pdb=" O GLN D 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 177 through 179 removed outlier: 7.183A pdb=" N ILE E 148 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER A 603 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASN E 146 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS A 605 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL E 144 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG E 74 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE E 148 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL E 72 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS E 213 " --> pdb=" O ASP E 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 739 through 742 removed outlier: 8.400A pdb=" N MET A 740 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE A 714 " --> pdb=" O MET A 740 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N TYR A 742 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 716 " --> pdb=" O TYR A 742 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 670 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 766 " --> pdb=" O ILE A 824 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 675 through 676 removed outlier: 6.398A pdb=" N HIS A 675 " --> pdb=" O SER A 692 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 966 through 967 Processing sheet with id=AB2, first strand: chain 'A' and resid 1137 through 1140 removed outlier: 3.833A pdb=" N LYS A1137 " --> pdb=" O TYR A1149 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A1147 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ARG A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 994 through 997 removed outlier: 6.600A pdb=" N VAL A1035 " --> pdb=" O ILE A 995 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A1036 " --> pdb=" O THR A1028 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1270 through 1273 removed outlier: 3.707A pdb=" N TYR A1312 " --> pdb=" O PHE A1270 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS A1272 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A1310 " --> pdb=" O LYS A1272 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 37 removed outlier: 8.966A pdb=" N PHE E 32 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N VAL E 46 " --> pdb=" O PHE E 32 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N TYR E 34 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 10.323A pdb=" N GLN E 44 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR E 36 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 198 through 199 removed outlier: 3.668A pdb=" N LYS E 198 " --> pdb=" O LYS E 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 23 through 24 removed outlier: 6.456A pdb=" N ARG F 23 " --> pdb=" O LYS G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 88 through 89 removed outlier: 6.871A pdb=" N LEU F 88 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS F 102 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 172 through 173 removed outlier: 3.502A pdb=" N VAL F 155 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE F 185 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU F 156 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AC3, first strand: chain 'F' and resid 336 through 338 removed outlier: 7.074A pdb=" N VAL F 296 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N GLY F 255 " --> pdb=" O SER F 295 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ASP F 297 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU F 257 " --> pdb=" O ASP F 297 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LYS F 213 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N LEU F 258 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA F 215 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ILE G 65 " --> pdb=" O THR F 482 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS F 484 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ILE G 67 " --> pdb=" O LYS F 484 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR G 64 " --> pdb=" O TYR G 60 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE G 57 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE G 85 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N CYS G 59 " --> pdb=" O CYS G 83 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N CYS G 83 " --> pdb=" O CYS G 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 343 through 347 removed outlier: 3.538A pdb=" N VAL F 435 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY F 445 " --> pdb=" O SER F 460 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 3.89 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.38: 6836 1.38 - 1.57: 11338 1.57 - 1.76: 57 1.76 - 1.95: 108 1.95 - 2.14: 12 Bond restraints: 18351 Sorted by residual: bond pdb=" C4' DCP A1604 " pdb=" O4' DCP A1604 " ideal model delta sigma weight residual 1.444 1.615 -0.171 1.00e-02 1.00e+04 2.91e+02 bond pdb=" C3' DCP A1604 " pdb=" C4' DCP A1604 " ideal model delta sigma weight residual 1.527 1.347 0.180 1.10e-02 8.26e+03 2.68e+02 bond pdb=" C4 DCP A1604 " pdb=" N4 DCP A1604 " ideal model delta sigma weight residual 1.334 1.473 -0.139 1.20e-02 6.94e+03 1.34e+02 bond pdb=" C1' DCP A1604 " pdb=" O4' DCP A1604 " ideal model delta sigma weight residual 1.418 1.305 0.113 1.20e-02 6.94e+03 8.86e+01 bond pdb=" C5 DCP A1604 " pdb=" C6 DCP A1604 " ideal model delta sigma weight residual 1.345 1.503 -0.158 1.80e-02 3.09e+03 7.69e+01 ... (remaining 18346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 24915 3.47 - 6.95: 69 6.95 - 10.42: 5 10.42 - 13.89: 1 13.89 - 17.37: 26 Bond angle restraints: 25016 Sorted by residual: angle pdb=" PB DCP A1604 " pdb=" O3B DCP A1604 " pdb=" PG DCP A1604 " ideal model delta sigma weight residual 139.87 124.01 15.86 1.00e+00 1.00e+00 2.52e+02 angle pdb=" PA DCP A1604 " pdb=" O3A DCP A1604 " pdb=" PB DCP A1604 " ideal model delta sigma weight residual 136.83 124.92 11.91 1.00e+00 1.00e+00 1.42e+02 angle pdb="FE3 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 91.07 -17.37 1.50e+00 4.44e-01 1.34e+02 angle pdb="FE1 SF4 A1601 " pdb=" S2 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.62 -16.92 1.50e+00 4.44e-01 1.27e+02 angle pdb="FE1 SF4 A1601 " pdb=" S3 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.59 -16.89 1.50e+00 4.44e-01 1.27e+02 ... (remaining 25011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 10036 16.93 - 33.86: 681 33.86 - 50.79: 167 50.79 - 67.72: 38 67.72 - 84.65: 10 Dihedral angle restraints: 10932 sinusoidal: 4425 harmonic: 6507 Sorted by residual: dihedral pdb=" CA SER A 220 " pdb=" C SER A 220 " pdb=" N PRO A 221 " pdb=" CA PRO A 221 " ideal model delta harmonic sigma weight residual 180.00 -146.10 -33.90 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA PHE A 772 " pdb=" C PHE A 772 " pdb=" N SER A 773 " pdb=" CA SER A 773 " ideal model delta harmonic sigma weight residual 180.00 -147.97 -32.03 0 5.00e+00 4.00e-02 4.10e+01 dihedral pdb=" CA LYS F 36 " pdb=" C LYS F 36 " pdb=" N SER F 37 " pdb=" CA SER F 37 " ideal model delta harmonic sigma weight residual 180.00 154.39 25.61 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 10929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.047: 2854 4.047 - 8.095: 0 8.095 - 12.142: 0 12.142 - 16.189: 0 16.189 - 20.237: 4 Chirality restraints: 2858 Sorted by residual: chirality pdb="FE3 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb=" S2 SF4 A1601 " pdb=" S4 SF4 A1601 " both_signs ideal model delta sigma weight residual False -10.55 9.68 -20.24 2.00e-01 2.50e+01 1.02e+04 chirality pdb="FE1 SF4 A1601 " pdb=" S2 SF4 A1601 " pdb=" S3 SF4 A1601 " pdb=" S4 SF4 A1601 " both_signs ideal model delta sigma weight residual False -10.55 9.60 -20.15 2.00e-01 2.50e+01 1.02e+04 chirality pdb="FE2 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb=" S3 SF4 A1601 " pdb=" S4 SF4 A1601 " both_signs ideal model delta sigma weight residual False 10.55 -9.59 20.14 2.00e-01 2.50e+01 1.01e+04 ... (remaining 2855 not shown) Planarity restraints: 3046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 341 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO F 342 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 342 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 342 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 683 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.41e+00 pdb=" N PRO A 684 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 684 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 684 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1352 " 0.031 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO A1353 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A1353 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1353 " 0.026 5.00e-02 4.00e+02 ... (remaining 3043 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 375 2.67 - 3.23: 16835 3.23 - 3.79: 27018 3.79 - 4.34: 38556 4.34 - 4.90: 63890 Nonbonded interactions: 146674 Sorted by model distance: nonbonded pdb=" O GLY A1162 " pdb=" O HOH A1701 " model vdw 2.117 3.040 nonbonded pdb=" O VAL F 122 " pdb=" OG1 THR F 126 " model vdw 2.131 3.040 nonbonded pdb=" OD1 ASP A 685 " pdb=" O HOH A1702 " model vdw 2.221 3.040 nonbonded pdb=" O SER A 170 " pdb=" OG SER A 173 " model vdw 2.245 3.040 nonbonded pdb=" O PHE D 114 " pdb=" O HOH D 301 " model vdw 2.258 3.040 ... (remaining 146669 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.060 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.180 18355 Z= 0.337 Angle : 0.879 46.658 25028 Z= 0.482 Chirality : 0.755 20.237 2858 Planarity : 0.004 0.058 3046 Dihedral : 12.665 84.650 6708 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.96 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.16), residues: 2160 helix: -0.36 (0.17), residues: 757 sheet: -2.31 (0.27), residues: 280 loop : -2.96 (0.15), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 237 TYR 0.017 0.001 TYR D 16 PHE 0.019 0.001 PHE G 94 TRP 0.010 0.001 TRP A 881 HIS 0.007 0.001 HIS F 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.34 (18351) covalent geometry : angle 0.74695 / 0.48 (25016) hydrogen bonds : bond 0.16084 / 11.09 ( 702) hydrogen bonds : angle 6.49225 / 4.62 ( 2002) metal coordination : bond 0.04993 / 2.57 ( 4) metal coordination : angle 21.19686 / 14.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7859 (mt0) cc_final: 0.7654 (mt0) REVERT: A 784 ILE cc_start: 0.9075 (mm) cc_final: 0.8794 (mm) REVERT: A 951 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8386 (tttm) REVERT: A 994 MET cc_start: 0.8217 (mtm) cc_final: 0.8004 (mtm) REVERT: A 1087 LEU cc_start: 0.8784 (tp) cc_final: 0.8580 (tp) REVERT: A 1142 ASP cc_start: 0.7542 (t0) cc_final: 0.7224 (t0) REVERT: D 135 ASN cc_start: 0.7474 (p0) cc_final: 0.6944 (p0) REVERT: D 142 GLU cc_start: 0.8218 (tt0) cc_final: 0.7866 (tt0) REVERT: E 1 MET cc_start: 0.6658 (mmt) cc_final: 0.6021 (mmp) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.1238 time to fit residues: 55.2111 Evaluate side-chains 220 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0060 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 212 ASN A 239 GLN A 251 ASN A 288 HIS A 319 GLN A 342 GLN A 866 ASN A1002 ASN A1206 GLN A1228 GLN A1368 ASN D 122 ASN D 214 GLN F 221 ASN F 245 ASN F 246 ASN G 77 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.097983 restraints weight = 48771.218| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.47 r_work: 0.3079 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.265 18355 Z= 0.250 Angle : 1.454 50.647 25028 Z= 0.826 Chirality : 0.241 6.408 2858 Planarity : 0.005 0.052 3046 Dihedral : 10.803 64.525 2647 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.73 % Allowed : 6.94 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.17), residues: 2160 helix: 0.76 (0.19), residues: 762 sheet: -1.85 (0.28), residues: 275 loop : -2.43 (0.16), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 158 TYR 0.024 0.001 TYR F 419 PHE 0.011 0.001 PHE G 94 TRP 0.014 0.001 TRP A 210 HIS 0.004 0.001 HIS F 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.25 (18351) covalent geometry : angle 1.28769 / 0.82 (25016) hydrogen bonds : bond 0.04435 / 3.04 ( 702) hydrogen bonds : angle 5.04813 / 3.69 ( 2002) metal coordination : bond 0.06576 / 3.23 ( 4) metal coordination : angle 30.84295 / 18.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 220 time to evaluate : 0.577 Fit side-chains REVERT: A 98 HIS cc_start: 0.7759 (t70) cc_final: 0.7530 (t-90) REVERT: A 784 ILE cc_start: 0.9107 (mm) cc_final: 0.8826 (mm) REVERT: A 951 LYS cc_start: 0.8661 (ttpp) cc_final: 0.8428 (tttm) REVERT: A 994 MET cc_start: 0.8637 (mtm) cc_final: 0.8416 (mtm) REVERT: D 135 ASN cc_start: 0.7379 (p0) cc_final: 0.6900 (p0) REVERT: E 1 MET cc_start: 0.6612 (mmt) cc_final: 0.5979 (mmp) REVERT: F 297 ASP cc_start: 0.8160 (m-30) cc_final: 0.7947 (m-30) outliers start: 13 outliers final: 10 residues processed: 227 average time/residue: 0.1270 time to fit residues: 44.7080 Evaluate side-chains 212 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 1456 ASP Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 89 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 142 optimal weight: 0.0970 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.098219 restraints weight = 47598.852| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.46 r_work: 0.3073 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 18355 Z= 0.245 Angle : 1.445 50.540 25028 Z= 0.822 Chirality : 0.241 6.377 2858 Planarity : 0.004 0.050 3046 Dihedral : 10.816 65.708 2647 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.95 % Allowed : 7.27 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.18), residues: 2160 helix: 1.17 (0.19), residues: 765 sheet: -1.53 (0.28), residues: 284 loop : -2.27 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1487 TYR 0.018 0.001 TYR D 16 PHE 0.013 0.001 PHE F 185 TRP 0.012 0.001 TRP F 76 HIS 0.004 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.24 (18351) covalent geometry : angle 1.27822 / 0.82 (25016) hydrogen bonds : bond 0.04110 / 2.77 ( 702) hydrogen bonds : angle 4.78561 / 3.51 ( 2002) metal coordination : bond 0.04411 / 2.19 ( 4) metal coordination : angle 30.75588 / 18.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.671 Fit side-chains REVERT: A 784 ILE cc_start: 0.9112 (mm) cc_final: 0.8818 (mm) REVERT: A 951 LYS cc_start: 0.8658 (ttpp) cc_final: 0.8435 (tttm) REVERT: D 135 ASN cc_start: 0.7640 (p0) cc_final: 0.7214 (p0) REVERT: E 1 MET cc_start: 0.6604 (mmt) cc_final: 0.5978 (mmp) outliers start: 17 outliers final: 10 residues processed: 212 average time/residue: 0.1143 time to fit residues: 39.4737 Evaluate side-chains 204 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 22 optimal weight: 7.9990 chunk 109 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.097201 restraints weight = 44267.086| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.34 r_work: 0.3062 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (12 function evaluations) r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 18355 Z= 0.252 Angle : 1.447 50.497 25028 Z= 0.823 Chirality : 0.241 6.370 2858 Planarity : 0.005 0.089 3046 Dihedral : 10.836 64.258 2647 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.06 % Allowed : 8.89 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.18), residues: 2160 helix: 1.35 (0.19), residues: 766 sheet: -1.35 (0.28), residues: 292 loop : -2.10 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 173 TYR 0.018 0.001 TYR D 16 PHE 0.011 0.001 PHE D 114 TRP 0.011 0.001 TRP F 76 HIS 0.005 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.25 (18351) covalent geometry : angle 1.28094 / 0.82 (25016) hydrogen bonds : bond 0.04118 / 2.76 ( 702) hydrogen bonds : angle 4.64352 / 3.39 ( 2002) metal coordination : bond 0.03973 / 1.96 ( 4) metal coordination : angle 30.71645 / 18.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.663 Fit side-chains REVERT: A 951 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8437 (tttm) REVERT: D 135 ASN cc_start: 0.7480 (p0) cc_final: 0.6937 (p0) REVERT: E 1 MET cc_start: 0.6649 (mmt) cc_final: 0.5988 (mmp) outliers start: 19 outliers final: 15 residues processed: 212 average time/residue: 0.1230 time to fit residues: 41.3906 Evaluate side-chains 207 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 1100 PHE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 107 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093812 restraints weight = 38013.258| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.13 r_work: 0.3011 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 18355 Z= 0.312 Angle : 1.476 50.526 25028 Z= 0.837 Chirality : 0.242 6.387 2858 Planarity : 0.005 0.091 3046 Dihedral : 11.045 66.644 2647 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.93 % Favored : 92.02 % Rotamer: Outliers : 1.90 % Allowed : 8.89 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.18), residues: 2160 helix: 1.25 (0.19), residues: 766 sheet: -1.54 (0.26), residues: 322 loop : -2.02 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1447 TYR 0.019 0.002 TYR E 16 PHE 0.014 0.002 PHE F 345 TRP 0.012 0.002 TRP F 103 HIS 0.009 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.31 (18351) covalent geometry : angle 1.31520 / 0.84 (25016) hydrogen bonds : bond 0.04824 / 3.24 ( 702) hydrogen bonds : angle 4.77691 / 3.49 ( 2002) metal coordination : bond 0.04703 / 2.32 ( 4) metal coordination : angle 30.60011 / 18.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.696 Fit side-chains REVERT: A 951 LYS cc_start: 0.8699 (ttpp) cc_final: 0.8440 (tttm) REVERT: D 135 ASN cc_start: 0.7583 (p0) cc_final: 0.7004 (p0) REVERT: E 1 MET cc_start: 0.6923 (mmt) cc_final: 0.6320 (mmp) outliers start: 34 outliers final: 23 residues processed: 217 average time/residue: 0.1148 time to fit residues: 40.3294 Evaluate side-chains 204 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1100 PHE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 0.0670 chunk 117 optimal weight: 0.0980 chunk 168 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 183 optimal weight: 0.0000 chunk 127 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 overall best weight: 0.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1032 ASN A1368 ASN F 245 ASN F 246 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.099153 restraints weight = 33135.260| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.96 r_work: 0.3103 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 18355 Z= 0.231 Angle : 1.442 50.492 25028 Z= 0.821 Chirality : 0.240 6.365 2858 Planarity : 0.004 0.075 3046 Dihedral : 10.830 63.134 2647 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.01 % Allowed : 11.02 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.18), residues: 2160 helix: 1.59 (0.19), residues: 767 sheet: -1.11 (0.29), residues: 286 loop : -1.90 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 791 TYR 0.018 0.001 TYR A 880 PHE 0.017 0.001 PHE D 114 TRP 0.012 0.001 TRP A 155 HIS 0.004 0.000 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.23 (18351) covalent geometry : angle 1.27463 / 0.82 (25016) hydrogen bonds : bond 0.03743 / 2.52 ( 702) hydrogen bonds : angle 4.52758 / 3.30 ( 2002) metal coordination : bond 0.03093 / 1.54 ( 4) metal coordination : angle 30.82320 / 18.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.566 Fit side-chains REVERT: A 747 GLU cc_start: 0.8435 (mp0) cc_final: 0.8198 (mp0) REVERT: A 951 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8421 (tttm) REVERT: A 1087 LEU cc_start: 0.9010 (tp) cc_final: 0.8736 (tp) REVERT: D 30 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: D 135 ASN cc_start: 0.7637 (p0) cc_final: 0.7227 (p0) REVERT: E 1 MET cc_start: 0.6566 (mmt) cc_final: 0.6030 (mmp) outliers start: 18 outliers final: 11 residues processed: 209 average time/residue: 0.1174 time to fit residues: 39.6556 Evaluate side-chains 204 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 60 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 51 optimal weight: 0.0670 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1368 ASN F 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.093712 restraints weight = 46498.957| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.37 r_work: 0.3005 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 18355 Z= 0.290 Angle : 1.468 50.531 25028 Z= 0.833 Chirality : 0.241 6.376 2858 Planarity : 0.005 0.084 3046 Dihedral : 10.967 65.106 2647 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.17 % Allowed : 11.24 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2160 helix: 1.45 (0.19), residues: 766 sheet: -1.14 (0.29), residues: 275 loop : -1.88 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 791 TYR 0.018 0.001 TYR E 16 PHE 0.013 0.001 PHE F 345 TRP 0.011 0.001 TRP F 76 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.29 (18351) covalent geometry : angle 1.30579 / 0.83 (25016) hydrogen bonds : bond 0.04520 / 3.01 ( 702) hydrogen bonds : angle 4.65034 / 3.39 ( 2002) metal coordination : bond 0.04132 / 2.04 ( 4) metal coordination : angle 30.63158 / 18.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.690 Fit side-chains REVERT: A 747 GLU cc_start: 0.8534 (mp0) cc_final: 0.8298 (mp0) REVERT: A 823 MET cc_start: 0.9269 (mmm) cc_final: 0.9033 (mmt) REVERT: A 951 LYS cc_start: 0.8710 (ttpp) cc_final: 0.8434 (tttm) REVERT: A 1087 LEU cc_start: 0.9072 (tp) cc_final: 0.8801 (tp) REVERT: D 135 ASN cc_start: 0.7827 (p0) cc_final: 0.7286 (p0) REVERT: E 1 MET cc_start: 0.6856 (mmt) cc_final: 0.6266 (mmp) outliers start: 21 outliers final: 18 residues processed: 200 average time/residue: 0.1167 time to fit residues: 37.7520 Evaluate side-chains 199 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 1100 PHE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 30 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.096602 restraints weight = 28564.066| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.78 r_work: 0.3066 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 18355 Z= 0.262 Angle : 1.454 50.499 25028 Z= 0.827 Chirality : 0.241 6.373 2858 Planarity : 0.005 0.075 3046 Dihedral : 10.987 63.508 2647 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.17 % Allowed : 11.52 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.18), residues: 2160 helix: 1.50 (0.19), residues: 766 sheet: -1.07 (0.30), residues: 275 loop : -1.86 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 791 TYR 0.017 0.001 TYR D 16 PHE 0.015 0.001 PHE D 114 TRP 0.011 0.001 TRP F 76 HIS 0.005 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.26 (18351) covalent geometry : angle 1.29064 / 0.83 (25016) hydrogen bonds : bond 0.04237 / 2.84 ( 702) hydrogen bonds : angle 4.61230 / 3.36 ( 2002) metal coordination : bond 0.03715 / 1.84 ( 4) metal coordination : angle 30.64945 / 18.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.722 Fit side-chains REVERT: A 747 GLU cc_start: 0.8416 (mp0) cc_final: 0.8185 (mp0) REVERT: A 951 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8417 (tttm) REVERT: A 1087 LEU cc_start: 0.9022 (tp) cc_final: 0.8738 (tp) REVERT: D 135 ASN cc_start: 0.7800 (p0) cc_final: 0.7312 (p0) REVERT: E 1 MET cc_start: 0.6813 (mmt) cc_final: 0.6246 (mmp) outliers start: 21 outliers final: 18 residues processed: 196 average time/residue: 0.1098 time to fit residues: 35.0913 Evaluate side-chains 199 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 1100 PHE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 180 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 90 optimal weight: 0.0270 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096863 restraints weight = 37763.860| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.11 r_work: 0.3057 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 18355 Z= 0.243 Angle : 1.448 50.489 25028 Z= 0.824 Chirality : 0.240 6.362 2858 Planarity : 0.004 0.076 3046 Dihedral : 10.908 63.198 2647 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.95 % Allowed : 11.86 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.18), residues: 2160 helix: 1.58 (0.19), residues: 768 sheet: -1.02 (0.30), residues: 275 loop : -1.80 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 791 TYR 0.018 0.001 TYR D 16 PHE 0.016 0.001 PHE D 114 TRP 0.012 0.001 TRP A 155 HIS 0.006 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.24 (18351) covalent geometry : angle 1.28262 / 0.82 (25016) hydrogen bonds : bond 0.03959 / 2.65 ( 702) hydrogen bonds : angle 4.54913 / 3.31 ( 2002) metal coordination : bond 0.03310 / 1.64 ( 4) metal coordination : angle 30.69806 / 18.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.596 Fit side-chains REVERT: A 358 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.8183 (t-90) REVERT: A 951 LYS cc_start: 0.8694 (ttpp) cc_final: 0.8423 (tttm) REVERT: A 1087 LEU cc_start: 0.9047 (tp) cc_final: 0.8749 (tp) REVERT: D 135 ASN cc_start: 0.7781 (p0) cc_final: 0.7318 (p0) REVERT: E 1 MET cc_start: 0.6699 (mmt) cc_final: 0.6191 (mmp) outliers start: 17 outliers final: 14 residues processed: 198 average time/residue: 0.1100 time to fit residues: 35.3637 Evaluate side-chains 199 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 183 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 169 optimal weight: 0.0770 chunk 139 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.095469 restraints weight = 37484.308| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.09 r_work: 0.3041 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 18355 Z= 0.272 Angle : 1.461 50.519 25028 Z= 0.829 Chirality : 0.241 6.371 2858 Planarity : 0.005 0.077 3046 Dihedral : 10.940 63.537 2647 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.17 % Allowed : 11.97 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.18), residues: 2160 helix: 1.49 (0.19), residues: 766 sheet: -1.02 (0.30), residues: 279 loop : -1.81 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 791 TYR 0.020 0.001 TYR D 16 PHE 0.014 0.001 PHE D 114 TRP 0.011 0.001 TRP F 76 HIS 0.008 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.27 (18351) covalent geometry : angle 1.29832 / 0.83 (25016) hydrogen bonds : bond 0.04212 / 2.81 ( 702) hydrogen bonds : angle 4.59530 / 3.34 ( 2002) metal coordination : bond 0.03632 / 1.79 ( 4) metal coordination : angle 30.63680 / 18.60 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.498 Fit side-chains REVERT: A 951 LYS cc_start: 0.8732 (ttpp) cc_final: 0.8467 (tttm) REVERT: A 1087 LEU cc_start: 0.9043 (tp) cc_final: 0.8755 (tp) REVERT: D 135 ASN cc_start: 0.7794 (p0) cc_final: 0.7285 (p0) REVERT: E 1 MET cc_start: 0.6763 (mmt) cc_final: 0.6262 (mmp) outliers start: 21 outliers final: 18 residues processed: 194 average time/residue: 0.1120 time to fit residues: 35.2015 Evaluate side-chains 196 residues out of total 2027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.094073 restraints weight = 35495.837| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.01 r_work: 0.3017 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 18355 Z= 0.321 Angle : 1.481 50.545 25028 Z= 0.839 Chirality : 0.242 6.384 2858 Planarity : 0.005 0.080 3046 Dihedral : 11.080 63.953 2647 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 1.17 % Allowed : 12.19 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.10 % 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: -0.83 (0.18), residues: 2160 helix: 1.34 (0.19), residues: 766 sheet: -1.25 (0.28), residues: 297 loop : -1.80 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 791 TYR 0.020 0.002 TYR D 16 PHE 0.013 0.002 PHE F 345 TRP 0.012 0.001 TRP F 103 HIS 0.021 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00848 / 0.32 (18351) covalent geometry : angle 1.32073 / 0.84 (25016) hydrogen bonds : bond 0.04670 / 3.12 ( 702) hydrogen bonds : angle 4.70671 / 3.43 ( 2002) metal coordination : bond 0.04111 / 2.03 ( 4) metal coordination : angle 30.58362 / 18.55 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4539.78 seconds wall clock time: 78 minutes 23.78 seconds (4703.78 seconds total)