Starting phenix.real_space_refine on Fri Sep 27 01:28:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8p_21108/09_2024/6v8p_21108.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8p_21108/09_2024/6v8p_21108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8p_21108/09_2024/6v8p_21108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8p_21108/09_2024/6v8p_21108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8p_21108/09_2024/6v8p_21108.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8p_21108/09_2024/6v8p_21108.cif" } resolution = 4.1 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= 0.012 sd= 0.089 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 36 5.16 5 C 9428 2.51 5 N 2446 2.21 5 O 2634 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 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14548 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1190, 8319 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 288} Link IDs: {'PTRANS': 58, 'TRANS': 1131} Chain breaks: 13 Unresolved non-hydrogen bonds: 1436 Unresolved non-hydrogen angles: 1787 Unresolved non-hydrogen dihedrals: 1137 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'GLN:plan1': 29, 'HIS:plan': 3, 'TYR:plan': 9, 'ASN:plan1': 15, 'ASP:plan': 38, 'PHE:plan': 6, 'GLU:plan': 64, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 736 Conformer: "B" Number of residues, atoms: 1190, 8319 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 288} Link IDs: {'PTRANS': 58, 'TRANS': 1131} Chain breaks: 13 Unresolved non-hydrogen bonds: 1436 Unresolved non-hydrogen angles: 1787 Unresolved non-hydrogen dihedrals: 1137 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'GLN:plan1': 29, 'HIS:plan': 3, 'TYR:plan': 9, 'ASN:plan1': 15, 'ASP:plan': 38, 'PHE:plan': 6, 'GLU:plan': 64, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 736 bond proxies already assigned to first conformer: 8519 Chain: "D" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1095 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 2 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 115 Chain: "E" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1445 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 117 Chain: "F" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 2917 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 26, 'TRANS': 433} Chain breaks: 4 Unresolved non-hydrogen bonds: 796 Unresolved non-hydrogen angles: 991 Unresolved non-hydrogen dihedrals: 661 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 1, 'TYR:plan': 9, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 26, 'PHE:plan': 8, 'GLU:plan': 24, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 464 Chain: "G" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 759 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8218 SG CYS A1473 32.544 59.992 83.144 1.00138.14 S ATOM 8044 SG CYS A1449 37.379 55.609 83.762 1.00132.78 S ATOM 8181 SG CYS A1468 31.202 54.299 85.357 1.00132.62 S ATOM 8024 SG CYS A1446 32.667 55.000 79.017 1.00136.80 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN A1259 " occ=0.50 ... (8 atoms not shown) pdb=" CB BGLN A1259 " occ=0.50 Time building chain proxies: 12.39, per 1000 atoms: 0.85 Number of scatterers: 14548 At special positions: 0 Unit cell: (80.301, 146.302, 171.602, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 36 16.00 O 2634 8.00 N 2446 7.00 C 9428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.90 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 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 23 sheets defined 38.5% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 95 through 116 removed outlier: 3.647A pdb=" N GLN A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 179 removed outlier: 3.809A pdb=" N SER A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 removed outlier: 3.526A pdb=" N PHE A 203 " --> pdb=" O TRP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.991A pdb=" N THR A 233 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.559A pdb=" N LEU A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 540 removed outlier: 4.135A pdb=" N ASN A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.911A pdb=" N TYR A 563 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA A 564 " --> pdb=" O LYS A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 564' Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 725 through 735 Processing helix chain 'A' and resid 744 through 760 Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.631A pdb=" N ALA A 794 " --> pdb=" O VAL A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 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 896 removed outlier: 3.976A pdb=" N LEU A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 889 " --> pdb=" O ALA A 885 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 892 " --> pdb=" O ASN A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 920 through 934 removed outlier: 3.579A pdb=" N VAL A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 949 Processing helix chain 'A' and resid 978 through 988 Processing helix chain 'A' and resid 1019 through 1024 Processing helix chain 'A' and resid 1044 through 1066 Processing helix chain 'A' and resid 1071 through 1095 removed outlier: 3.759A pdb=" N LYS A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR A1093 " --> pdb=" O ALA A1089 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY A1094 " --> pdb=" O ASN A1090 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1130 removed outlier: 3.563A pdb=" N ALA A1110 " --> pdb=" O CYS A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1171 removed outlier: 3.614A pdb=" N ALA A1158 " --> pdb=" O THR A1154 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A1159 " --> pdb=" O ALA A1155 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER A1160 " --> pdb=" O ILE A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1241 removed outlier: 3.904A pdb=" N GLN A1228 " --> pdb=" O ILE A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1261 removed outlier: 3.751A pdb=" N ILE A1247 " --> pdb=" O ASP A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1335 removed outlier: 3.761A pdb=" N PHE A1333 " --> pdb=" O SER A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1361 Proline residue: A1353 - end of helix removed outlier: 4.372A pdb=" N LEU A1361 " --> pdb=" O ARG A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1372 removed outlier: 3.505A pdb=" N GLU A1372 " --> pdb=" O ASN A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1455 removed outlier: 4.289A pdb=" N ARG A1452 " --> pdb=" O THR A1448 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR A1453 " --> pdb=" O CYS A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1466 Processing helix chain 'A' and resid 1473 through 1487 removed outlier: 3.996A pdb=" N TYR A1477 " --> pdb=" O CYS A1473 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 23 removed outlier: 4.166A pdb=" N LYS D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 68 removed outlier: 3.723A pdb=" N LYS D 68 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.700A pdb=" N VAL D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 24 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 Processing helix chain 'E' and resid 109 through 130 removed outlier: 3.797A pdb=" N LYS E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 175 removed outlier: 3.796A pdb=" N LYS E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 0 through 9 Processing helix chain 'F' and resid 30 through 34 removed outlier: 4.133A pdb=" N TYR F 34 " --> pdb=" O ASP F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 76 Processing helix chain 'F' and resid 92 through 96 removed outlier: 3.741A pdb=" N ILE F 96 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 124 Processing helix chain 'F' and resid 132 through 138 removed outlier: 3.789A pdb=" N TYR F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 241 Processing helix chain 'F' and resid 247 through 252 Processing helix chain 'F' and resid 272 through 291 removed outlier: 3.735A pdb=" N LEU F 276 " --> pdb=" O ASN F 272 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 327 removed outlier: 4.367A pdb=" N SER F 326 " --> pdb=" O SER F 323 " (cutoff:3.500A) 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 removed outlier: 3.534A pdb=" N THR F 415 " --> pdb=" O THR F 411 " (cutoff:3.500A) 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 removed outlier: 3.585A pdb=" N ILE A 25 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 35 removed outlier: 8.453A pdb=" N ILE A 268 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 72 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE A 270 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N HIS A 74 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 163 removed outlier: 3.718A pdb=" N ASP A 139 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ILE A 938 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE A 146 " --> pdb=" O ILE A 938 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 581 through 582 removed outlier: 6.555A pdb=" N ILE A 581 " --> pdb=" O GLN D 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 177 through 179 removed outlier: 7.469A pdb=" N ILE E 148 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER A 603 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASN E 146 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS A 605 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL E 144 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE E 148 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL E 72 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASN E 81 " --> pdb=" O CYS E 87 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS E 87 " --> pdb=" O ASN E 81 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLN E 214 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL E 203 " --> pdb=" O GLN E 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 670 through 676 removed outlier: 3.548A pdb=" N CYS A 697 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS A 675 " --> pdb=" O MET A 693 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 693 " --> pdb=" O HIS A 675 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N SER A 692 " --> pdb=" O VAL A 717 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N MET A 740 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 714 " --> pdb=" O MET A 740 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TYR A 742 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 716 " --> pdb=" O TYR A 742 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 763 through 764 Processing sheet with id=AA9, first strand: chain 'A' and resid 959 through 960 removed outlier: 4.523A pdb=" N GLY A1141 " --> pdb=" O MET A 960 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A1147 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY A1141 " --> pdb=" O SER A1145 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER A1145 " --> pdb=" O GLY A1141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 966 through 967 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 971 through 976 current: chain 'A' and resid 1210 through 1214 Processing sheet with id=AB2, first strand: chain 'A' and resid 994 through 997 removed outlier: 6.486A pdb=" N VAL A1035 " --> pdb=" O ILE A 995 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1006 through 1008 Processing sheet with id=AB4, first strand: chain 'A' and resid 1270 through 1274 removed outlier: 3.943A pdb=" N ILE A1310 " --> pdb=" O VAL A1274 " (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 'D' and resid 139 through 145 removed outlier: 3.771A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN D 81 " --> pdb=" O CYS D 87 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS D 87 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS D 90 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU D 217 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE D 215 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 37 removed outlier: 9.091A pdb=" N PHE E 32 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N VAL E 46 " --> pdb=" O PHE E 32 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N TYR E 34 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N GLN E 44 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR E 36 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 23 through 24 removed outlier: 5.608A 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: 7.082A pdb=" N LEU F 88 " --> pdb=" O TRP F 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 172 through 173 removed outlier: 3.519A pdb=" N GLY F 106 " --> pdb=" O VAL F 173 " (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: 3.699A pdb=" N SER F 295 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS F 213 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N LEU F 258 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA F 215 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 343 through 347 removed outlier: 7.092A pdb=" N ASP F 351 " --> pdb=" O VAL F 435 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE F 437 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU F 353 " --> pdb=" O ILE F 437 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA F 439 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL F 355 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLN F 441 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR F 436 " --> pdb=" O ILE F 459 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL F 461 " --> pdb=" O TYR F 436 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL F 438 " --> pdb=" O VAL F 461 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY F 445 " --> pdb=" O SER F 460 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 20 through 21 removed outlier: 5.752A pdb=" N CYS G 83 " --> pdb=" O CYS G 59 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N CYS G 59 " --> pdb=" O CYS G 83 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE G 85 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE G 57 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS G 58 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS G 66 " --> pdb=" O CYS G 58 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.64 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.41: 6192 1.41 - 1.59: 8650 1.59 - 1.78: 0 1.78 - 1.96: 36 1.96 - 2.14: 12 Bond restraints: 14890 Sorted by residual: bond pdb=" S1 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.106 0.174 3.00e-02 1.11e+03 3.36e+01 bond pdb=" S3 SF4 A1601 " pdb="FE2 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.67e+01 bond pdb=" S1 SF4 A1601 " pdb="FE3 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.66e+01 bond pdb=" S3 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.65e+01 bond pdb=" S2 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.126 0.154 3.00e-02 1.11e+03 2.65e+01 ... (remaining 14885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 20373 3.50 - 6.99: 51 6.99 - 10.49: 2 10.49 - 13.98: 2 13.98 - 17.48: 24 Bond angle restraints: 20452 Sorted by residual: angle pdb="FE3 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 91.18 -17.48 1.50e+00 4.44e-01 1.36e+02 angle pdb="FE1 SF4 A1601 " pdb=" S4 SF4 A1601 " pdb="FE3 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="FE2 SF4 A1601 " pdb=" S1 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 angle pdb="FE1 SF4 A1601 " pdb=" S3 SF4 A1601 " pdb="FE2 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.57 -16.87 1.50e+00 4.44e-01 1.27e+02 angle pdb="FE1 SF4 A1601 " pdb=" S4 SF4 A1601 " pdb="FE2 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.55 -16.85 1.50e+00 4.44e-01 1.26e+02 ... (remaining 20447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 7962 14.89 - 29.78: 569 29.78 - 44.67: 142 44.67 - 59.56: 14 59.56 - 74.45: 2 Dihedral angle restraints: 8689 sinusoidal: 2445 harmonic: 6244 Sorted by residual: dihedral pdb=" CA PHE A1181 " pdb=" C PHE A1181 " pdb=" N GLU A1182 " pdb=" CA GLU A1182 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C ASP D 94 " pdb=" N ASP D 94 " pdb=" CA ASP D 94 " pdb=" CB ASP D 94 " ideal model delta harmonic sigma weight residual -122.60 -132.34 9.74 0 2.50e+00 1.60e-01 1.52e+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 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 8686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.048: 2453 4.048 - 8.096: 0 8.096 - 12.144: 0 12.144 - 16.192: 0 16.192 - 20.240: 4 Chirality restraints: 2457 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 9.61 -20.16 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 -9.60 20.16 2.00e-01 2.50e+01 1.02e+04 ... (remaining 2454 not shown) Planarity restraints: 2636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 285 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C LYS F 285 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS F 285 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE F 286 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 91 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C TYR D 91 " 0.038 2.00e-02 2.50e+03 pdb=" O TYR D 91 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL D 92 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 561 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 562 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 562 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 562 " 0.026 5.00e-02 4.00e+02 ... (remaining 2633 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1572 2.75 - 3.29: 14490 3.29 - 3.82: 22633 3.82 - 4.36: 24131 4.36 - 4.90: 43391 Nonbonded interactions: 106217 Sorted by model distance: nonbonded pdb=" O SER A 170 " pdb=" OG SER A 173 " model vdw 2.210 3.040 nonbonded pdb=" O ILE A 78 " pdb=" OH TYR A 195 " model vdw 2.252 3.040 nonbonded pdb=" O ASP A1456 " pdb=" ND2 ASN A1461 " model vdw 2.271 3.120 nonbonded pdb=" O TYR A1093 " pdb=" OG1 THR A1096 " model vdw 2.272 3.040 nonbonded pdb=" O THR F 411 " pdb=" OG1 THR F 415 " model vdw 2.287 3.040 ... (remaining 106212 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 43.770 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.005 0.174 14890 Z= 0.353 Angle : 0.756 17.478 20452 Z= 0.468 Chirality : 0.815 20.240 2457 Planarity : 0.003 0.047 2636 Dihedral : 11.303 74.451 4615 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.74 % Favored : 93.21 % Rotamer: Outliers : 0.29 % Allowed : 2.42 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.58 (0.17), residues: 2066 helix: -0.14 (0.18), residues: 764 sheet: -2.09 (0.28), residues: 263 loop : -2.94 (0.16), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 881 HIS 0.004 0.000 HIS A 287 PHE 0.007 0.001 PHE A1181 TYR 0.011 0.001 TYR A 880 ARG 0.004 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 207 time to evaluate : 1.611 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1232 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 1368 ASN cc_start: 0.9310 (m-40) cc_final: 0.9027 (m110) REVERT: D 40 PHE cc_start: 0.8509 (m-80) cc_final: 0.7989 (m-80) REVERT: D 214 GLN cc_start: 0.8883 (tt0) cc_final: 0.8676 (tm-30) REVERT: E 23 TYR cc_start: 0.8717 (m-80) cc_final: 0.8443 (m-80) REVERT: E 32 PHE cc_start: 0.9154 (m-80) cc_final: 0.8579 (m-10) REVERT: E 37 TYR cc_start: 0.8426 (t80) cc_final: 0.8197 (t80) REVERT: E 163 ASP cc_start: 0.8677 (m-30) cc_final: 0.8224 (p0) REVERT: G 103 GLN cc_start: 0.8289 (mt0) cc_final: 0.8019 (mp10) outliers start: 3 outliers final: 1 residues processed: 209 average time/residue: 0.2039 time to fit residues: 70.6239 Evaluate side-chains 140 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 20.0000 chunk 159 optimal weight: 8.9990 chunk 88 optimal weight: 0.0770 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 overall best weight: 3.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 ASN A1115 GLN A1206 GLN D 71 HIS E 122 ASN F 55 HIS F 198 GLN F 434 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.259 14890 Z= 0.562 Angle : 1.397 50.358 20452 Z= 0.901 Chirality : 0.258 6.369 2457 Planarity : 0.004 0.050 2636 Dihedral : 3.861 25.871 2203 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.41 (0.18), residues: 2066 helix: 1.05 (0.19), residues: 764 sheet: -1.72 (0.27), residues: 282 loop : -2.36 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 210 HIS 0.005 0.001 HIS A 770 PHE 0.026 0.002 PHE A 927 TYR 0.016 0.002 TYR A 387 ARG 0.020 0.001 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.732 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1232 " (corrupted residue). Skipping it. REVERT: A 878 LEU cc_start: 0.9299 (mp) cc_final: 0.9041 (tt) REVERT: A 975 ASP cc_start: 0.8530 (t0) cc_final: 0.8223 (t0) REVERT: A 1368 ASN cc_start: 0.9384 (m-40) cc_final: 0.9138 (m110) REVERT: D 50 ARG cc_start: 0.8515 (mtm110) cc_final: 0.7934 (mtm-85) REVERT: E 21 LEU cc_start: 0.9601 (mt) cc_final: 0.9308 (mt) REVERT: E 25 ASN cc_start: 0.9329 (t0) cc_final: 0.9069 (t0) REVERT: E 32 PHE cc_start: 0.9337 (m-80) cc_final: 0.8795 (m-10) REVERT: E 37 TYR cc_start: 0.8352 (t80) cc_final: 0.8090 (t80) REVERT: E 122 ASN cc_start: 0.9535 (m-40) cc_final: 0.9276 (m110) REVERT: E 163 ASP cc_start: 0.8620 (m-30) cc_final: 0.8094 (p0) REVERT: F 272 ASN cc_start: 0.8976 (t0) cc_final: 0.8475 (t0) REVERT: F 347 TYR cc_start: 0.9292 (m-10) cc_final: 0.9018 (m-10) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1911 time to fit residues: 50.3559 Evaluate side-chains 124 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 170 optimal weight: 30.0000 chunk 189 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 153 optimal weight: 10.0000 overall best weight: 4.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 165 ASN A 560 ASN A1172 ASN F 198 GLN ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.237 14890 Z= 0.542 Angle : 1.426 50.600 20452 Z= 0.916 Chirality : 0.260 6.380 2457 Planarity : 0.005 0.063 2636 Dihedral : 4.472 28.421 2203 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.10 % Allowed : 4.36 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.02 (0.18), residues: 2066 helix: 1.16 (0.19), residues: 762 sheet: -1.16 (0.29), residues: 273 loop : -2.04 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 210 HIS 0.010 0.002 HIS F 55 PHE 0.023 0.002 PHE E 45 TYR 0.023 0.002 TYR A 563 ARG 0.004 0.001 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.615 Fit side-chains revert: symmetry clash REVERT: A 822 HIS cc_start: 0.8428 (m-70) cc_final: 0.7746 (m90) REVERT: A 878 LEU cc_start: 0.9374 (mp) cc_final: 0.9085 (tt) REVERT: D 114 PHE cc_start: 0.9324 (t80) cc_final: 0.9054 (t80) REVERT: E 37 TYR cc_start: 0.8263 (t80) cc_final: 0.7908 (t80) REVERT: E 44 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8336 (tm-30) REVERT: E 122 ASN cc_start: 0.9645 (m-40) cc_final: 0.9310 (m110) REVERT: F 272 ASN cc_start: 0.9260 (t0) cc_final: 0.9041 (t0) REVERT: G 97 TYR cc_start: 0.8863 (t80) cc_final: 0.8523 (t80) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1818 time to fit residues: 43.0629 Evaluate side-chains 110 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 202 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 HIS A1206 GLN F 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.242 14890 Z= 0.601 Angle : 1.465 51.131 20452 Z= 0.935 Chirality : 0.259 6.385 2457 Planarity : 0.005 0.059 2636 Dihedral : 5.025 29.929 2203 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.06 (0.18), residues: 2066 helix: 0.88 (0.19), residues: 769 sheet: -1.00 (0.31), residues: 227 loop : -1.90 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 210 HIS 0.009 0.002 HIS F 55 PHE 0.020 0.002 PHE E 32 TYR 0.022 0.002 TYR E 34 ARG 0.004 0.001 ARG A 918 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8784 (mmm) cc_final: 0.8564 (mmm) REVERT: A 878 LEU cc_start: 0.9380 (mp) cc_final: 0.9178 (tt) REVERT: E 37 TYR cc_start: 0.8152 (t80) cc_final: 0.7771 (t80) REVERT: F 427 PHE cc_start: 0.9321 (m-80) cc_final: 0.8891 (m-80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1784 time to fit residues: 40.0867 Evaluate side-chains 98 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.0970 chunk 115 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 151 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 173 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 182 optimal weight: 0.0060 chunk 51 optimal weight: 5.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1006 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 14890 Z= 0.497 Angle : 1.387 50.494 20452 Z= 0.895 Chirality : 0.258 6.330 2457 Planarity : 0.004 0.056 2636 Dihedral : 4.310 29.180 2203 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.44 (0.19), residues: 2066 helix: 1.60 (0.19), residues: 762 sheet: -0.61 (0.31), residues: 230 loop : -1.71 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 8 HIS 0.004 0.001 HIS F 288 PHE 0.016 0.001 PHE G 94 TYR 0.018 0.001 TYR A 523 ARG 0.003 0.000 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.827 Fit side-chains REVERT: A 34 MET cc_start: 0.8764 (mmm) cc_final: 0.8439 (mmm) REVERT: A 84 ILE cc_start: 0.9444 (pt) cc_final: 0.9228 (mm) REVERT: A 600 MET cc_start: 0.9099 (mmm) cc_final: 0.8644 (mmp) REVERT: A 822 HIS cc_start: 0.8324 (m-70) cc_final: 0.7716 (m90) REVERT: A 1157 GLU cc_start: 0.9530 (mt-10) cc_final: 0.9163 (pt0) REVERT: E 32 PHE cc_start: 0.9087 (m-80) cc_final: 0.8463 (m-80) REVERT: E 37 TYR cc_start: 0.7891 (t80) cc_final: 0.7563 (t80) REVERT: E 44 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8063 (tm-30) REVERT: E 122 ASN cc_start: 0.9593 (m-40) cc_final: 0.9104 (m110) REVERT: F 66 GLU cc_start: 0.9395 (tm-30) cc_final: 0.9051 (tm-30) REVERT: F 272 ASN cc_start: 0.9105 (t0) cc_final: 0.8510 (t0) REVERT: F 274 ASP cc_start: 0.8788 (m-30) cc_final: 0.8027 (m-30) REVERT: G 97 TYR cc_start: 0.8799 (t80) cc_final: 0.8407 (t80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1906 time to fit residues: 50.5016 Evaluate side-chains 116 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 16 optimal weight: 0.0000 chunk 67 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 overall best weight: 3.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 ASN E 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.238 14890 Z= 0.524 Angle : 1.404 50.674 20452 Z= 0.904 Chirality : 0.258 6.339 2457 Planarity : 0.004 0.055 2636 Dihedral : 4.397 27.516 2203 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.39 (0.19), residues: 2066 helix: 1.60 (0.19), residues: 764 sheet: -0.71 (0.30), residues: 242 loop : -1.62 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 210 HIS 0.004 0.001 HIS F 288 PHE 0.012 0.001 PHE A 927 TYR 0.017 0.002 TYR A 387 ARG 0.004 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 600 MET cc_start: 0.9077 (mmm) cc_final: 0.8618 (mmp) REVERT: A 822 HIS cc_start: 0.8408 (m-70) cc_final: 0.7909 (m90) REVERT: A 1157 GLU cc_start: 0.9527 (mt-10) cc_final: 0.9166 (pt0) REVERT: E 32 PHE cc_start: 0.8992 (m-80) cc_final: 0.8694 (m-10) REVERT: E 37 TYR cc_start: 0.8049 (t80) cc_final: 0.7733 (t80) REVERT: E 44 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8054 (tm-30) REVERT: F 66 GLU cc_start: 0.9406 (tm-30) cc_final: 0.9091 (tm-30) REVERT: F 272 ASN cc_start: 0.9256 (t0) cc_final: 0.8739 (t0) REVERT: F 274 ASP cc_start: 0.8839 (m-30) cc_final: 0.8282 (m-30) REVERT: F 427 PHE cc_start: 0.9249 (m-80) cc_final: 0.8840 (m-80) REVERT: G 97 TYR cc_start: 0.8826 (t80) cc_final: 0.8415 (t80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1740 time to fit residues: 41.0077 Evaluate side-chains 107 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 20.0000 chunk 22 optimal weight: 0.0010 chunk 115 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 202 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 overall best weight: 4.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN E 49 ASN F 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 14890 Z= 0.544 Angle : 1.418 50.766 20452 Z= 0.910 Chirality : 0.260 6.390 2457 Planarity : 0.005 0.053 2636 Dihedral : 4.711 31.507 2203 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.53 (0.19), residues: 2066 helix: 1.43 (0.19), residues: 771 sheet: -0.54 (0.33), residues: 213 loop : -1.72 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 199 HIS 0.005 0.001 HIS A 74 PHE 0.020 0.001 PHE A 772 TYR 0.018 0.002 TYR A 387 ARG 0.005 0.001 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8700 (mmm) cc_final: 0.8473 (mmm) REVERT: A 600 MET cc_start: 0.9096 (mmm) cc_final: 0.8632 (mmp) REVERT: A 822 HIS cc_start: 0.8437 (m-70) cc_final: 0.8042 (m90) REVERT: E 32 PHE cc_start: 0.9014 (m-80) cc_final: 0.8707 (m-10) REVERT: E 37 TYR cc_start: 0.8067 (t80) cc_final: 0.7775 (t80) REVERT: E 44 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8068 (tm-30) REVERT: F 66 GLU cc_start: 0.9415 (tm-30) cc_final: 0.9096 (tm-30) REVERT: F 272 ASN cc_start: 0.9309 (t0) cc_final: 0.8876 (t0) REVERT: F 274 ASP cc_start: 0.8846 (m-30) cc_final: 0.8404 (m-30) REVERT: F 427 PHE cc_start: 0.9280 (m-80) cc_final: 0.8844 (m-80) REVERT: G 97 TYR cc_start: 0.8811 (t80) cc_final: 0.8355 (t80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1827 time to fit residues: 40.2891 Evaluate side-chains 101 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 137 optimal weight: 0.0980 chunk 100 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.235 14890 Z= 0.525 Angle : 1.407 50.599 20452 Z= 0.905 Chirality : 0.259 6.390 2457 Planarity : 0.004 0.053 2636 Dihedral : 4.565 29.730 2203 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.45 (0.19), residues: 2066 helix: 1.54 (0.19), residues: 773 sheet: -0.46 (0.34), residues: 211 loop : -1.73 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 199 HIS 0.004 0.001 HIS A 287 PHE 0.015 0.001 PHE E 32 TYR 0.016 0.001 TYR A 387 ARG 0.003 0.000 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8550 (mmm) cc_final: 0.8335 (mmm) REVERT: A 84 ILE cc_start: 0.9432 (pt) cc_final: 0.9110 (mm) REVERT: A 600 MET cc_start: 0.9104 (mmm) cc_final: 0.8657 (mmp) REVERT: A 822 HIS cc_start: 0.8411 (m-70) cc_final: 0.8049 (m90) REVERT: E 32 PHE cc_start: 0.8781 (m-80) cc_final: 0.8468 (m-10) REVERT: E 37 TYR cc_start: 0.8094 (t80) cc_final: 0.7797 (t80) REVERT: F 66 GLU cc_start: 0.9421 (tm-30) cc_final: 0.9103 (tm-30) REVERT: F 272 ASN cc_start: 0.9273 (t0) cc_final: 0.8827 (t0) REVERT: F 274 ASP cc_start: 0.8831 (m-30) cc_final: 0.8437 (m-30) REVERT: F 427 PHE cc_start: 0.9296 (m-80) cc_final: 0.8853 (m-80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2034 time to fit residues: 42.7655 Evaluate side-chains 105 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.2980 chunk 176 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 30.0000 chunk 178 optimal weight: 20.0000 chunk 187 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.241 14890 Z= 0.499 Angle : 1.386 50.490 20452 Z= 0.894 Chirality : 0.258 6.331 2457 Planarity : 0.004 0.053 2636 Dihedral : 4.270 30.603 2203 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.18 (0.19), residues: 2066 helix: 1.84 (0.20), residues: 768 sheet: -0.39 (0.32), residues: 243 loop : -1.63 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 199 HIS 0.003 0.001 HIS A 283 PHE 0.014 0.001 PHE E 75 TYR 0.016 0.001 TYR E 27 ARG 0.003 0.000 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8601 (mmm) cc_final: 0.8380 (mmm) REVERT: A 84 ILE cc_start: 0.9477 (pt) cc_final: 0.9233 (mm) REVERT: A 600 MET cc_start: 0.9092 (mmm) cc_final: 0.8693 (mmp) REVERT: A 822 HIS cc_start: 0.8437 (m-70) cc_final: 0.7876 (m90) REVERT: A 823 MET cc_start: 0.7784 (mtm) cc_final: 0.7497 (ptp) REVERT: A 1153 LYS cc_start: 0.8644 (mptt) cc_final: 0.8375 (mmtm) REVERT: E 32 PHE cc_start: 0.8745 (m-80) cc_final: 0.8474 (m-10) REVERT: E 37 TYR cc_start: 0.8011 (t80) cc_final: 0.7683 (t80) REVERT: E 44 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7949 (tm-30) REVERT: F 66 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9067 (tm-30) REVERT: F 272 ASN cc_start: 0.9186 (t0) cc_final: 0.8672 (t0) REVERT: F 274 ASP cc_start: 0.8776 (m-30) cc_final: 0.8348 (m-30) REVERT: F 427 PHE cc_start: 0.9228 (m-80) cc_final: 0.8839 (m-80) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1970 time to fit residues: 46.7083 Evaluate side-chains 111 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 9.9990 chunk 121 optimal weight: 0.0980 chunk 94 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 209 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 128 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 132 optimal weight: 40.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.230 14890 Z= 0.532 Angle : 1.408 50.602 20452 Z= 0.906 Chirality : 0.259 6.359 2457 Planarity : 0.004 0.053 2636 Dihedral : 4.461 29.867 2203 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.32 (0.19), residues: 2066 helix: 1.68 (0.19), residues: 773 sheet: -0.37 (0.34), residues: 206 loop : -1.68 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 210 HIS 0.005 0.001 HIS A 287 PHE 0.014 0.001 PHE A1147 TYR 0.017 0.002 TYR A 387 ARG 0.003 0.000 ARG D 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8533 (mmm) cc_final: 0.8316 (mmm) REVERT: A 84 ILE cc_start: 0.9400 (pt) cc_final: 0.9120 (mm) REVERT: A 600 MET cc_start: 0.9112 (mmm) cc_final: 0.8713 (mmp) REVERT: A 822 HIS cc_start: 0.8495 (m-70) cc_final: 0.8005 (m90) REVERT: D 50 ARG cc_start: 0.8864 (mtm-85) cc_final: 0.8531 (mtm-85) REVERT: E 32 PHE cc_start: 0.8744 (m-80) cc_final: 0.8484 (m-10) REVERT: E 37 TYR cc_start: 0.8127 (t80) cc_final: 0.7815 (t80) REVERT: E 44 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8034 (tm-30) REVERT: F 66 GLU cc_start: 0.9442 (tm-30) cc_final: 0.9117 (tm-30) REVERT: F 272 ASN cc_start: 0.9277 (t0) cc_final: 0.8817 (t0) REVERT: F 274 ASP cc_start: 0.8853 (m-30) cc_final: 0.8472 (m-30) REVERT: F 427 PHE cc_start: 0.9283 (m-80) cc_final: 0.8828 (m-80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1898 time to fit residues: 39.2024 Evaluate side-chains 103 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.0050 chunk 51 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 24 optimal weight: 0.0670 chunk 46 optimal weight: 7.9990 chunk 166 optimal weight: 0.1980 chunk 69 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 overall best weight: 1.0536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.051835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.042693 restraints weight = 89621.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.043903 restraints weight = 52818.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.044848 restraints weight = 37043.393| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.240 14890 Z= 0.494 Angle : 1.384 50.505 20452 Z= 0.893 Chirality : 0.258 6.350 2457 Planarity : 0.004 0.053 2636 Dihedral : 4.175 29.725 2203 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.09 (0.19), residues: 2066 helix: 1.91 (0.20), residues: 767 sheet: -0.15 (0.32), residues: 236 loop : -1.61 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 8 HIS 0.003 0.001 HIS F 288 PHE 0.015 0.001 PHE E 75 TYR 0.016 0.001 TYR E 12 ARG 0.003 0.000 ARG A1057 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2411.40 seconds wall clock time: 44 minutes 1.21 seconds (2641.21 seconds total)