Starting phenix.real_space_refine on Sat Sep 28 04:14:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/09_2024/6v93_21115.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/09_2024/6v93_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/09_2024/6v93_21115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/09_2024/6v93_21115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/09_2024/6v93_21115.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/09_2024/6v93_21115.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 11, 'ASP:plan': 18, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 35, 'ARG:plan': 8} 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: {'GLN:plan1': 11, 'ASP:plan': 18, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 35, 'ARG:plan': 8} 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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 13, 'GLU:plan': 13, 'ARG:plan': 2} 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: 15.13, per 1000 atoms: 0.84 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: 5.05 Conformation dependent library (CDL) restraints added in 3.2 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: 5.92 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: 7.20 Time building geometry restraints manager: 5.72 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: 24916 3.47 - 6.95: 68 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: 10049 16.93 - 33.86: 691 33.86 - 50.79: 168 50.79 - 67.72: 38 67.72 - 84.65: 10 Dihedral angle restraints: 10956 sinusoidal: 4449 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 10953 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: 6.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 55.750 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.100 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 18351 Z= 0.392 Angle : 0.738 17.368 25016 Z= 0.461 Chirality : 0.755 20.237 2858 Planarity : 0.004 0.058 3046 Dihedral : 12.686 84.650 6732 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.82 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP A 881 HIS 0.007 0.001 HIS F 316 PHE 0.019 0.001 PHE G 94 TYR 0.017 0.001 TYR D 16 ARG 0.003 0.000 ARG F 237 *********************** 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 fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 2.224 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: 0.3141 time to fit residues: 137.1384 Evaluate side-chains 220 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 111 optimal weight: 0.0870 chunk 88 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.250 18351 Z= 0.506 Angle : 1.290 50.174 25016 Z= 0.824 Chirality : 0.244 6.492 2858 Planarity : 0.005 0.058 3046 Dihedral : 10.866 66.218 2671 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.84 % Allowed : 6.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2160 helix: 0.70 (0.19), residues: 766 sheet: -1.91 (0.27), residues: 296 loop : -2.42 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 210 HIS 0.004 0.001 HIS F 316 PHE 0.013 0.001 PHE G 94 TYR 0.022 0.001 TYR F 419 ARG 0.007 0.001 ARG E 158 *********************** 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 230 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 215 time to evaluate : 2.216 Fit side-chains REVERT: A 52 GLN cc_start: 0.7963 (mt0) cc_final: 0.7737 (mt0) REVERT: A 98 HIS cc_start: 0.7739 (t70) cc_final: 0.7535 (t-90) REVERT: A 784 ILE cc_start: 0.9070 (mm) cc_final: 0.8785 (mm) REVERT: A 1087 LEU cc_start: 0.8754 (tp) cc_final: 0.8541 (tp) REVERT: D 135 ASN cc_start: 0.7418 (p0) cc_final: 0.6916 (p0) REVERT: E 1 MET cc_start: 0.6755 (mmt) cc_final: 0.6146 (mmp) outliers start: 15 outliers final: 12 residues processed: 224 average time/residue: 0.3095 time to fit residues: 107.4130 Evaluate side-chains 210 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 198 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS 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 1063 THR Chi-restraints excluded: chain A residue 1100 PHE 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 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 110 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 199 optimal weight: 8.9990 chunk 215 optimal weight: 0.0020 chunk 177 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS F 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 18351 Z= 0.524 Angle : 1.297 50.522 25016 Z= 0.827 Chirality : 0.242 6.404 2858 Planarity : 0.005 0.055 3046 Dihedral : 10.929 67.227 2671 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.29 % Allowed : 7.94 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 2160 helix: 1.04 (0.19), residues: 767 sheet: -1.70 (0.26), residues: 308 loop : -2.27 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 76 HIS 0.016 0.001 HIS A 44 PHE 0.014 0.001 PHE F 185 TYR 0.018 0.001 TYR E 16 ARG 0.005 0.001 ARG A1447 *********************** 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 221 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 2.006 Fit side-chains REVERT: A 784 ILE cc_start: 0.9066 (mm) cc_final: 0.8765 (mm) REVERT: D 135 ASN cc_start: 0.7383 (p0) cc_final: 0.6850 (p0) REVERT: E 1 MET cc_start: 0.6905 (mmt) cc_final: 0.6341 (mmp) REVERT: F 419 TYR cc_start: 0.5882 (t80) cc_final: 0.5418 (m-10) REVERT: G 21 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8695 (mt) outliers start: 23 outliers final: 16 residues processed: 212 average time/residue: 0.2696 time to fit residues: 91.8438 Evaluate side-chains 207 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 2.184 ------------------------------------------------------------------------------- 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 1063 THR Chi-restraints excluded: chain A residue 1100 PHE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 77 ILE 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 G residue 20 VAL Chi-restraints excluded: chain G residue 21 LEU 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 196 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 199 optimal weight: 0.4980 chunk 211 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1032 ASN G 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 18351 Z= 0.547 Angle : 1.308 50.507 25016 Z= 0.832 Chirality : 0.242 6.396 2858 Planarity : 0.005 0.091 3046 Dihedral : 10.990 67.914 2671 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 1.68 % Allowed : 8.95 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2160 helix: 1.18 (0.19), residues: 764 sheet: -1.57 (0.27), residues: 308 loop : -2.11 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 103 HIS 0.006 0.001 HIS A 105 PHE 0.015 0.001 PHE D 114 TYR 0.018 0.001 TYR E 16 ARG 0.006 0.001 ARG E 158 *********************** 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 218 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 1.973 Fit side-chains REVERT: D 135 ASN cc_start: 0.7418 (p0) cc_final: 0.6828 (p0) REVERT: G 21 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8765 (mt) outliers start: 30 outliers final: 20 residues processed: 210 average time/residue: 0.2802 time to fit residues: 93.1121 Evaluate side-chains 198 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 2.324 ------------------------------------------------------------------------------- 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 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 168 ILE Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 21 LEU 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 176 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS F 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 18351 Z= 0.483 Angle : 1.285 50.487 25016 Z= 0.823 Chirality : 0.241 6.364 2858 Planarity : 0.005 0.086 3046 Dihedral : 10.813 67.656 2671 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.40 % Allowed : 10.57 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.18), residues: 2160 helix: 1.38 (0.19), residues: 766 sheet: -1.41 (0.28), residues: 294 loop : -1.98 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 76 HIS 0.005 0.001 HIS A 358 PHE 0.016 0.001 PHE D 114 TYR 0.020 0.001 TYR F 127 ARG 0.003 0.000 ARG E 158 *********************** 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 210 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 1.925 Fit side-chains REVERT: A 358 HIS cc_start: 0.8304 (OUTLIER) cc_final: 0.8042 (t-90) REVERT: A 1087 LEU cc_start: 0.8822 (tp) cc_final: 0.8489 (tp) REVERT: D 135 ASN cc_start: 0.7410 (p0) cc_final: 0.6864 (p0) REVERT: E 1 MET cc_start: 0.6440 (mmp) cc_final: 0.6163 (mmp) REVERT: F 419 TYR cc_start: 0.5748 (t80) cc_final: 0.5119 (m-10) REVERT: G 21 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8673 (mt) outliers start: 25 outliers final: 17 residues processed: 203 average time/residue: 0.2672 time to fit residues: 86.5656 Evaluate side-chains 199 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS 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 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 371 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 21 LEU 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 71 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 211 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS F 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 : 0.007 0.244 18351 Z= 0.463 Angle : 1.277 50.482 25016 Z= 0.819 Chirality : 0.240 6.357 2858 Planarity : 0.004 0.078 3046 Dihedral : 10.646 67.583 2671 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.23 % Allowed : 11.52 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.18), residues: 2160 helix: 1.53 (0.19), residues: 766 sheet: -1.14 (0.29), residues: 285 loop : -1.91 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 155 HIS 0.015 0.001 HIS A 358 PHE 0.016 0.001 PHE D 114 TYR 0.017 0.001 TYR D 16 ARG 0.004 0.000 ARG E 158 *********************** 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 206 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 1.982 Fit side-chains REVERT: A 784 ILE cc_start: 0.9072 (mm) cc_final: 0.8771 (mm) REVERT: A 1049 MET cc_start: 0.7694 (ptm) cc_final: 0.7451 (ptm) REVERT: A 1087 LEU cc_start: 0.8834 (tp) cc_final: 0.8494 (tp) REVERT: D 135 ASN cc_start: 0.7413 (p0) cc_final: 0.6926 (p0) REVERT: E 1 MET cc_start: 0.6456 (mmp) cc_final: 0.6129 (mmp) REVERT: F 419 TYR cc_start: 0.5588 (t80) cc_final: 0.5100 (m-10) outliers start: 22 outliers final: 15 residues processed: 198 average time/residue: 0.2745 time to fit residues: 87.7548 Evaluate side-chains 196 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS 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 D residue 72 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 402 THR 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 204 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 211 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 18351 Z= 0.463 Angle : 1.275 50.489 25016 Z= 0.818 Chirality : 0.240 6.354 2858 Planarity : 0.004 0.076 3046 Dihedral : 10.503 67.431 2671 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.34 % Allowed : 11.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2160 helix: 1.62 (0.19), residues: 769 sheet: -1.11 (0.29), residues: 291 loop : -1.82 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 155 HIS 0.004 0.001 HIS A 288 PHE 0.015 0.001 PHE D 114 TYR 0.018 0.001 TYR D 16 ARG 0.006 0.000 ARG E 158 *********************** 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 213 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 2.054 Fit side-chains REVERT: D 135 ASN cc_start: 0.7587 (p0) cc_final: 0.7163 (p0) REVERT: E 1 MET cc_start: 0.6484 (mmp) cc_final: 0.6117 (mmp) REVERT: F 419 TYR cc_start: 0.5668 (t80) cc_final: 0.5335 (m-10) outliers start: 24 outliers final: 16 residues processed: 206 average time/residue: 0.2667 time to fit residues: 89.4987 Evaluate side-chains 201 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS 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 D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL 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 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 130 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 134 optimal weight: 0.0870 chunk 143 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 165 optimal weight: 4.9990 overall best weight: 1.1358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 0.243 18351 Z= 0.472 Angle : 1.281 50.493 25016 Z= 0.820 Chirality : 0.240 6.355 2858 Planarity : 0.004 0.074 3046 Dihedral : 10.511 67.124 2671 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.17 % Allowed : 12.25 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2160 helix: 1.63 (0.19), residues: 770 sheet: -0.93 (0.30), residues: 271 loop : -1.78 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 76 HIS 0.004 0.001 HIS A 288 PHE 0.015 0.001 PHE D 114 TYR 0.018 0.001 TYR D 16 ARG 0.006 0.000 ARG E 158 *********************** 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 204 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 2.001 Fit side-chains REVERT: D 135 ASN cc_start: 0.7589 (p0) cc_final: 0.7162 (p0) REVERT: E 1 MET cc_start: 0.6497 (mmp) cc_final: 0.6131 (mmp) REVERT: F 419 TYR cc_start: 0.5555 (t80) cc_final: 0.5291 (m-10) outliers start: 21 outliers final: 19 residues processed: 199 average time/residue: 0.2497 time to fit residues: 81.4080 Evaluate side-chains 200 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS 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 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 4 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 246 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 418 CYS 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 192 optimal weight: 1.9990 chunk 202 optimal weight: 0.0170 chunk 184 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 177 optimal weight: 0.4980 chunk 186 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 245 ASN F 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 18351 Z= 0.462 Angle : 1.277 50.477 25016 Z= 0.818 Chirality : 0.240 6.350 2858 Planarity : 0.004 0.073 3046 Dihedral : 10.458 66.736 2671 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.12 % Allowed : 12.70 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2160 helix: 1.69 (0.19), residues: 771 sheet: -0.87 (0.30), residues: 285 loop : -1.72 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 155 HIS 0.004 0.000 HIS A 288 PHE 0.016 0.001 PHE D 114 TYR 0.019 0.001 TYR D 16 ARG 0.005 0.000 ARG E 158 *********************** 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 204 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 1.867 Fit side-chains REVERT: D 135 ASN cc_start: 0.7590 (p0) cc_final: 0.7178 (p0) REVERT: E 1 MET cc_start: 0.6444 (mmp) cc_final: 0.6109 (mmp) outliers start: 20 outliers final: 17 residues processed: 199 average time/residue: 0.2784 time to fit residues: 90.1686 Evaluate side-chains 197 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS 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 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 402 THR Chi-restraints excluded: chain F residue 418 CYS 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 207 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 144 optimal weight: 0.0970 chunk 218 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 245 ASN F 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 18351 Z= 0.457 Angle : 1.272 50.464 25016 Z= 0.816 Chirality : 0.240 6.342 2858 Planarity : 0.004 0.070 3046 Dihedral : 10.311 66.409 2671 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.78 % Allowed : 13.26 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 2160 helix: 1.82 (0.19), residues: 770 sheet: -0.83 (0.30), residues: 288 loop : -1.66 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 155 HIS 0.003 0.000 HIS A 288 PHE 0.015 0.001 PHE D 114 TYR 0.020 0.001 TYR D 16 ARG 0.005 0.000 ARG E 158 ********************** 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 207 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 2.065 Fit side-chains REVERT: A 823 MET cc_start: 0.8973 (mmm) cc_final: 0.8729 (mmm) REVERT: A 1235 ILE cc_start: 0.9161 (mt) cc_final: 0.8960 (mm) REVERT: E 1 MET cc_start: 0.6349 (mmp) cc_final: 0.6041 (mmp) outliers start: 14 outliers final: 13 residues processed: 203 average time/residue: 0.2869 time to fit residues: 92.8508 Evaluate side-chains 191 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 178 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS 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 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 G residue 20 VAL 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 185 optimal weight: 0.5980 chunk 53 optimal weight: 0.0570 chunk 160 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 213 HIS F 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.097082 restraints weight = 52993.600| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.70 r_work: 0.3060 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 18351 Z= 0.458 Angle : 1.272 50.473 25016 Z= 0.816 Chirality : 0.240 6.346 2858 Planarity : 0.004 0.070 3046 Dihedral : 10.270 65.954 2671 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.89 % Allowed : 13.42 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 2160 helix: 1.86 (0.19), residues: 772 sheet: -0.75 (0.30), residues: 288 loop : -1.62 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 155 HIS 0.004 0.000 HIS A 288 PHE 0.015 0.001 PHE D 114 TYR 0.019 0.001 TYR D 16 ARG 0.004 0.000 ARG E 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3580.51 seconds wall clock time: 65 minutes 59.69 seconds (3959.69 seconds total)