Starting phenix.real_space_refine on Wed Mar 4 15:38:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v8p_21108/03_2026/6v8p_21108.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v8p_21108/03_2026/6v8p_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/cci-nas-00/data/ceres_data/6v8p_21108/03_2026/6v8p_21108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v8p_21108/03_2026/6v8p_21108.map" model { file = "/net/cci-nas-00/data/ceres_data/6v8p_21108/03_2026/6v8p_21108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v8p_21108/03_2026/6v8p_21108.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASP:plan': 38, 'TYR:plan': 9, 'ARG:plan': 35, 'GLN:plan1': 29, 'ASN:plan1': 15, 'GLU:plan': 64, 'PHE:plan': 6, 'HIS:plan': 3} 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: {'ASP:plan': 38, 'TYR:plan': 9, 'ARG:plan': 35, 'GLN:plan1': 29, 'ASN:plan1': 15, 'GLU:plan': 64, 'PHE:plan': 6, 'HIS:plan': 3} 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: {'ARG:plan': 2, 'GLU:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 5, 'GLN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'HIS:plan': 1} 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: {'ARG:plan': 7, 'GLU:plan': 15, 'ASP:plan': 6, 'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2} 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: {'ASP:plan': 26, 'PHE:plan': 8, 'ASN:plan1': 15, 'GLU:plan': 24, 'ARG:plan': 18, 'GLN:plan1': 12, 'TYR:plan': 9, 'TRP:plan': 2, 'HIS:plan': 1} 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: {'ASP:plan': 9, 'GLN:plan1': 4, 'GLU:plan': 3, 'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} 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: 4.48, per 1000 atoms: 0.31 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: 1.32 Conformation dependent library (CDL) restraints added in 1.0 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: 0.49 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: 2.68 Time building geometry restraints manager: 1.66 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.530 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.050 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.010 ------------------------------------------------------------------------------- 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 0.181 14894 Z= 0.212 Angle : 0.977 44.221 20464 Z= 0.471 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 : 3.93 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (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 ARG 0.004 0.000 ARG A 320 TYR 0.011 0.001 TYR A 880 PHE 0.007 0.001 PHE A1181 TRP 0.004 0.001 TRP A 881 HIS 0.004 0.000 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00505 (14890) covalent geometry : angle 0.75646 (20452) hydrogen bonds : bond 0.15529 ( 664) hydrogen bonds : angle 5.98685 ( 1918) metal coordination : bond 0.11016 ( 4) metal coordination : angle 25.57592 ( 12) *********************** 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 to be fit. rotamer outliers: 3 poor density : 207 time to evaluate : 0.402 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: 0.0855 time to fit residues: 29.8919 Evaluate side-chains 140 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 overall best weight: 3.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 ASN A1115 GLN A1173 ASN A1206 GLN D 71 HIS E 122 ASN F 55 HIS F 198 GLN F 434 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.055783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.046066 restraints weight = 90053.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.047407 restraints weight = 53876.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048379 restraints weight = 37408.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.049077 restraints weight = 28573.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.049567 restraints weight = 23303.519| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.236 14894 Z= 0.272 Angle : 1.587 50.330 20464 Z= 0.901 Chirality : 0.264 6.533 2457 Planarity : 0.004 0.049 2636 Dihedral : 3.813 25.075 2203 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.18), residues: 2066 helix: 1.01 (0.19), residues: 764 sheet: -1.72 (0.27), residues: 282 loop : -2.38 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 118 TYR 0.016 0.002 TYR A 387 PHE 0.027 0.001 PHE A 927 TRP 0.028 0.001 TRP A 210 HIS 0.004 0.001 HIS A 770 Details of bonding type rmsd covalent geometry : bond 0.00733 (14890) covalent geometry : angle 1.39331 (20452) hydrogen bonds : bond 0.03535 ( 664) hydrogen bonds : angle 4.52956 ( 1918) metal coordination : bond 0.02394 ( 4) metal coordination : angle 31.43531 ( 12) *********************** 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 to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.576 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1232 " (corrupted residue). Skipping it. REVERT: A 975 ASP cc_start: 0.8438 (t0) cc_final: 0.8142 (t0) REVERT: A 1368 ASN cc_start: 0.9343 (m-40) cc_final: 0.9108 (m110) REVERT: D 50 ARG cc_start: 0.8491 (mtm110) cc_final: 0.7958 (mtm-85) REVERT: E 32 PHE cc_start: 0.9281 (m-80) cc_final: 0.8717 (m-10) REVERT: E 37 TYR cc_start: 0.8371 (t80) cc_final: 0.8126 (t80) REVERT: E 122 ASN cc_start: 0.9488 (m-40) cc_final: 0.9227 (m110) REVERT: E 163 ASP cc_start: 0.8523 (m-30) cc_final: 0.8013 (p0) REVERT: F 272 ASN cc_start: 0.8990 (t0) cc_final: 0.8497 (t0) REVERT: F 347 TYR cc_start: 0.9197 (m-10) cc_final: 0.8923 (m-10) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.0828 time to fit residues: 21.8829 Evaluate side-chains 123 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 113 optimal weight: 5.9990 chunk 165 optimal weight: 0.0980 chunk 46 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 205 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 101 optimal weight: 0.0030 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.056487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.046684 restraints weight = 91340.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.048041 restraints weight = 54183.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.048854 restraints weight = 37728.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.049653 restraints weight = 29576.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.050142 restraints weight = 23937.432| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.250 14894 Z= 0.248 Angle : 1.565 50.637 20464 Z= 0.892 Chirality : 0.259 6.353 2457 Planarity : 0.004 0.058 2636 Dihedral : 3.707 25.991 2203 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.19), residues: 2066 helix: 1.43 (0.20), residues: 774 sheet: -1.25 (0.28), residues: 283 loop : -2.18 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 118 TYR 0.013 0.001 TYR E 57 PHE 0.029 0.001 PHE G 94 TRP 0.010 0.001 TRP A 210 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00713 (14890) covalent geometry : angle 1.37526 (20452) hydrogen bonds : bond 0.02922 ( 664) hydrogen bonds : angle 4.14505 ( 1918) metal coordination : bond 0.03118 ( 4) metal coordination : angle 30.88729 ( 12) *********************** 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 153 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1232 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 822 HIS cc_start: 0.8283 (m-70) cc_final: 0.7675 (m90) REVERT: A 878 LEU cc_start: 0.9274 (mp) cc_final: 0.9054 (tt) REVERT: A 1368 ASN cc_start: 0.9259 (m-40) cc_final: 0.9022 (m110) REVERT: D 214 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8414 (tm-30) REVERT: E 32 PHE cc_start: 0.8937 (m-80) cc_final: 0.7878 (m-80) REVERT: E 37 TYR cc_start: 0.8287 (t80) cc_final: 0.8064 (t80) REVERT: E 49 ASN cc_start: 0.8638 (t0) cc_final: 0.8161 (m-40) REVERT: E 163 ASP cc_start: 0.8537 (m-30) cc_final: 0.8038 (p0) REVERT: F 272 ASN cc_start: 0.8954 (t0) cc_final: 0.8499 (t0) outliers start: 1 outliers final: 1 residues processed: 153 average time/residue: 0.0766 time to fit residues: 20.2681 Evaluate side-chains 126 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 106 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 187 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 70 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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 785 HIS F 198 GLN F 332 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.051422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.041988 restraints weight = 93695.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.043215 restraints weight = 55878.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.043957 restraints weight = 38832.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.044662 restraints weight = 30611.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.045091 restraints weight = 25012.020| |-----------------------------------------------------------------------------| 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: 0.8334 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.237 14894 Z= 0.329 Angle : 1.632 50.728 20464 Z= 0.923 Chirality : 0.260 6.370 2457 Planarity : 0.005 0.056 2636 Dihedral : 4.527 26.796 2203 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.18), residues: 2066 helix: 1.27 (0.19), residues: 766 sheet: -0.92 (0.30), residues: 251 loop : -1.89 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 320 TYR 0.018 0.002 TYR A 742 PHE 0.030 0.002 PHE E 45 TRP 0.026 0.002 TRP A 210 HIS 0.009 0.002 HIS F 55 Details of bonding type rmsd covalent geometry : bond 0.00824 (14890) covalent geometry : angle 1.43726 (20452) hydrogen bonds : bond 0.03972 ( 664) hydrogen bonds : angle 4.62039 ( 1918) metal coordination : bond 0.01380 ( 4) metal coordination : angle 31.95842 ( 12) *********************** 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 138 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 822 HIS cc_start: 0.8245 (m-70) cc_final: 0.7653 (m90) REVERT: A 878 LEU cc_start: 0.9388 (mp) cc_final: 0.9076 (tt) REVERT: E 37 TYR cc_start: 0.8259 (t80) cc_final: 0.7891 (t80) REVERT: E 44 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8219 (tm-30) REVERT: E 49 ASN cc_start: 0.9093 (t0) cc_final: 0.8489 (m-40) REVERT: E 122 ASN cc_start: 0.9622 (m-40) cc_final: 0.9287 (m110) REVERT: F 272 ASN cc_start: 0.9311 (t0) cc_final: 0.9049 (t0) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.0800 time to fit residues: 19.1344 Evaluate side-chains 109 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 24 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 199 optimal weight: 8.9990 chunk 111 optimal weight: 0.3980 chunk 171 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.052735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.043221 restraints weight = 92195.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.044440 restraints weight = 54599.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.045380 restraints weight = 38423.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.046026 restraints weight = 29270.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.046561 restraints weight = 23846.750| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 14894 Z= 0.256 Angle : 1.580 50.517 20464 Z= 0.899 Chirality : 0.259 6.347 2457 Planarity : 0.004 0.055 2636 Dihedral : 4.228 28.967 2203 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 2066 helix: 1.62 (0.19), residues: 769 sheet: -0.85 (0.29), residues: 273 loop : -1.78 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1057 TYR 0.013 0.001 TYR A 880 PHE 0.016 0.001 PHE A 927 TRP 0.010 0.001 TRP A 210 HIS 0.004 0.001 HIS F 288 Details of bonding type rmsd covalent geometry : bond 0.00720 (14890) covalent geometry : angle 1.39002 (20452) hydrogen bonds : bond 0.03202 ( 664) hydrogen bonds : angle 4.23417 ( 1918) metal coordination : bond 0.01985 ( 4) metal coordination : angle 31.07314 ( 12) *********************** 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 146 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 HIS cc_start: 0.8230 (m-70) cc_final: 0.7683 (m90) REVERT: A 878 LEU cc_start: 0.9354 (mp) cc_final: 0.9124 (tt) REVERT: E 37 TYR cc_start: 0.8110 (t80) cc_final: 0.7729 (t80) REVERT: E 49 ASN cc_start: 0.8930 (t0) cc_final: 0.8341 (m-40) REVERT: E 122 ASN cc_start: 0.9570 (m-40) cc_final: 0.9236 (m110) REVERT: F 156 LEU cc_start: 0.9325 (mt) cc_final: 0.8876 (tt) REVERT: F 272 ASN cc_start: 0.9244 (t0) cc_final: 0.8966 (t0) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0788 time to fit residues: 19.8180 Evaluate side-chains 116 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 158 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 160 optimal weight: 20.0000 chunk 191 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A1172 ASN A1206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.040306 restraints weight = 95852.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.041422 restraints weight = 56371.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.042333 restraints weight = 39637.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.042916 restraints weight = 30053.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.043419 restraints weight = 24631.800| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.009 0.233 14894 Z= 0.352 Angle : 1.647 50.836 20464 Z= 0.930 Chirality : 0.260 6.399 2457 Planarity : 0.005 0.058 2636 Dihedral : 4.877 29.769 2203 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.19), residues: 2066 helix: 1.08 (0.19), residues: 778 sheet: -0.69 (0.32), residues: 218 loop : -1.81 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 97 TYR 0.021 0.002 TYR A 387 PHE 0.025 0.002 PHE E 45 TRP 0.027 0.002 TRP A 210 HIS 0.010 0.002 HIS F 55 Details of bonding type rmsd covalent geometry : bond 0.00857 (14890) covalent geometry : angle 1.45319 (20452) hydrogen bonds : bond 0.04137 ( 664) hydrogen bonds : angle 4.82903 ( 1918) metal coordination : bond 0.01857 ( 4) metal coordination : angle 32.05343 ( 12) *********************** 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 123 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 878 LEU cc_start: 0.9425 (mp) cc_final: 0.9194 (tt) REVERT: E 37 TYR cc_start: 0.8210 (t80) cc_final: 0.7842 (t80) REVERT: E 44 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8213 (tm-30) REVERT: E 49 ASN cc_start: 0.9083 (t0) cc_final: 0.8748 (m-40) REVERT: F 272 ASN cc_start: 0.9426 (t0) cc_final: 0.9132 (t0) REVERT: F 274 ASP cc_start: 0.8890 (m-30) cc_final: 0.8229 (m-30) REVERT: F 427 PHE cc_start: 0.9277 (m-80) cc_final: 0.8827 (m-80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0746 time to fit residues: 16.3563 Evaluate side-chains 97 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 7 optimal weight: 20.0000 chunk 4 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 121 optimal weight: 0.0670 chunk 37 optimal weight: 0.0060 chunk 93 optimal weight: 9.9990 chunk 50 optimal weight: 0.0970 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.052763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.043498 restraints weight = 89265.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.044797 restraints weight = 52490.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.045617 restraints weight = 36076.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.046359 restraints weight = 28049.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.046853 restraints weight = 22682.495| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 14894 Z= 0.249 Angle : 1.576 50.482 20464 Z= 0.897 Chirality : 0.258 6.311 2457 Planarity : 0.004 0.053 2636 Dihedral : 4.218 29.328 2203 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.19), residues: 2066 helix: 1.76 (0.19), residues: 759 sheet: -0.56 (0.30), residues: 254 loop : -1.59 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1057 TYR 0.014 0.001 TYR A 387 PHE 0.016 0.001 PHE A 741 TRP 0.011 0.001 TRP D 8 HIS 0.003 0.001 HIS F 288 Details of bonding type rmsd covalent geometry : bond 0.00715 (14890) covalent geometry : angle 1.38810 (20452) hydrogen bonds : bond 0.03017 ( 664) hydrogen bonds : angle 4.17793 ( 1918) metal coordination : bond 0.02016 ( 4) metal coordination : angle 30.85552 ( 12) *********************** 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 152 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.9390 (pt) cc_final: 0.9176 (mm) REVERT: A 600 MET cc_start: 0.9102 (mmm) cc_final: 0.8881 (mmp) REVERT: A 822 HIS cc_start: 0.8259 (m-70) cc_final: 0.7693 (m90) REVERT: A 1153 LYS cc_start: 0.8550 (mptt) cc_final: 0.8340 (mmtm) REVERT: E 37 TYR cc_start: 0.8020 (t80) cc_final: 0.7597 (t80) REVERT: E 44 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7826 (tm-30) REVERT: E 49 ASN cc_start: 0.8750 (t0) cc_final: 0.8244 (m-40) REVERT: E 122 ASN cc_start: 0.9538 (m-40) cc_final: 0.9050 (m110) REVERT: F 66 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8938 (tm-30) REVERT: F 272 ASN cc_start: 0.9216 (t0) cc_final: 0.8567 (t0) REVERT: F 274 ASP cc_start: 0.8684 (m-30) cc_final: 0.8142 (m-30) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0764 time to fit residues: 20.3169 Evaluate side-chains 115 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 119 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 31 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN F 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.049662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.040647 restraints weight = 96626.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.041790 restraints weight = 57815.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.042548 restraints weight = 40568.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.043178 restraints weight = 31679.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.043493 restraints weight = 26042.442| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.234 14894 Z= 0.332 Angle : 1.625 50.878 20464 Z= 0.922 Chirality : 0.259 6.375 2457 Planarity : 0.005 0.053 2636 Dihedral : 4.659 29.460 2203 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.19), residues: 2066 helix: 1.37 (0.19), residues: 778 sheet: -0.43 (0.33), residues: 216 loop : -1.67 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 118 TYR 0.020 0.002 TYR A 387 PHE 0.019 0.002 PHE E 45 TRP 0.022 0.002 TRP A 210 HIS 0.006 0.002 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00828 (14890) covalent geometry : angle 1.43748 (20452) hydrogen bonds : bond 0.03800 ( 664) hydrogen bonds : angle 4.63010 ( 1918) metal coordination : bond 0.01716 ( 4) metal coordination : angle 31.32286 ( 12) *********************** 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 116 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8944 (mmm) cc_final: 0.8735 (mmm) REVERT: A 600 MET cc_start: 0.9087 (mmm) cc_final: 0.8762 (mmp) REVERT: E 37 TYR cc_start: 0.8117 (t80) cc_final: 0.7815 (t80) REVERT: E 49 ASN cc_start: 0.8965 (t0) cc_final: 0.8746 (m-40) REVERT: F 272 ASN cc_start: 0.9401 (t0) cc_final: 0.9014 (t0) REVERT: F 274 ASP cc_start: 0.8857 (m-30) cc_final: 0.8415 (m-30) REVERT: F 427 PHE cc_start: 0.9155 (m-80) cc_final: 0.8802 (m-80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0745 time to fit residues: 15.4050 Evaluate side-chains 95 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 192 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 chunk 198 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 0.0070 chunk 173 optimal weight: 7.9990 chunk 163 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 overall best weight: 3.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.050588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.041520 restraints weight = 93757.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.042740 restraints weight = 55105.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.043641 restraints weight = 38093.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.044231 restraints weight = 28938.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.044736 restraints weight = 23724.690| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 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 = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.240 14894 Z= 0.271 Angle : 1.588 50.560 20464 Z= 0.905 Chirality : 0.259 6.388 2457 Planarity : 0.004 0.051 2636 Dihedral : 4.530 31.810 2203 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.19), residues: 2066 helix: 1.62 (0.19), residues: 771 sheet: -0.41 (0.34), residues: 209 loop : -1.62 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1057 TYR 0.016 0.001 TYR A 387 PHE 0.017 0.001 PHE E 45 TRP 0.016 0.001 TRP A 199 HIS 0.004 0.001 HIS F 288 Details of bonding type rmsd covalent geometry : bond 0.00741 (14890) covalent geometry : angle 1.40220 (20452) hydrogen bonds : bond 0.03332 ( 664) hydrogen bonds : angle 4.38670 ( 1918) metal coordination : bond 0.02600 ( 4) metal coordination : angle 30.85274 ( 12) *********************** 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 130 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8774 (mmm) cc_final: 0.8474 (mmm) REVERT: A 84 ILE cc_start: 0.9355 (pt) cc_final: 0.9118 (mm) REVERT: A 600 MET cc_start: 0.9090 (mmm) cc_final: 0.8770 (mmp) REVERT: A 822 HIS cc_start: 0.8316 (m-70) cc_final: 0.7737 (m90) REVERT: E 37 TYR cc_start: 0.8020 (t80) cc_final: 0.7635 (t80) REVERT: E 49 ASN cc_start: 0.9055 (t0) cc_final: 0.8461 (m-40) REVERT: F 66 GLU cc_start: 0.9270 (tm-30) cc_final: 0.8966 (tm-30) REVERT: F 272 ASN cc_start: 0.9317 (t0) cc_final: 0.8824 (t0) REVERT: F 274 ASP cc_start: 0.8786 (m-30) cc_final: 0.8318 (m-30) REVERT: F 427 PHE cc_start: 0.9236 (m-80) cc_final: 0.8849 (m-80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0776 time to fit residues: 17.7140 Evaluate side-chains 106 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 4 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 164 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 127 optimal weight: 0.0070 chunk 27 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 overall best weight: 3.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.050483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.041272 restraints weight = 94541.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.042520 restraints weight = 55083.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.043422 restraints weight = 37938.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.043925 restraints weight = 28793.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.044437 restraints weight = 24132.017| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 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 = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.236 14894 Z= 0.270 Angle : 1.587 50.592 20464 Z= 0.904 Chirality : 0.259 6.381 2457 Planarity : 0.004 0.051 2636 Dihedral : 4.429 30.902 2203 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 2066 helix: 1.66 (0.19), residues: 773 sheet: -0.31 (0.34), residues: 205 loop : -1.62 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1057 TYR 0.016 0.001 TYR A 387 PHE 0.019 0.001 PHE E 45 TRP 0.017 0.001 TRP A 199 HIS 0.005 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00739 (14890) covalent geometry : angle 1.40133 (20452) hydrogen bonds : bond 0.03276 ( 664) hydrogen bonds : angle 4.33811 ( 1918) metal coordination : bond 0.02700 ( 4) metal coordination : angle 30.82747 ( 12) ********************** 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 127 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8647 (mmm) cc_final: 0.8328 (mmm) REVERT: A 84 ILE cc_start: 0.9393 (pt) cc_final: 0.9138 (mm) REVERT: A 600 MET cc_start: 0.9098 (mmm) cc_final: 0.8779 (mmp) REVERT: A 822 HIS cc_start: 0.8392 (m-70) cc_final: 0.7987 (m90) REVERT: E 37 TYR cc_start: 0.8086 (t80) cc_final: 0.7719 (t80) REVERT: E 44 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8061 (tm-30) REVERT: E 49 ASN cc_start: 0.9032 (t0) cc_final: 0.8373 (m-40) REVERT: F 66 GLU cc_start: 0.9319 (tm-30) cc_final: 0.9000 (tm-30) REVERT: F 272 ASN cc_start: 0.9315 (t0) cc_final: 0.8831 (t0) REVERT: F 274 ASP cc_start: 0.8810 (m-30) cc_final: 0.8391 (m-30) REVERT: F 427 PHE cc_start: 0.9256 (m-80) cc_final: 0.8859 (m-80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0753 time to fit residues: 16.8776 Evaluate side-chains 108 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 155 optimal weight: 0.0020 chunk 21 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.050547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.041422 restraints weight = 93462.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.042655 restraints weight = 54391.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.043550 restraints weight = 37465.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.044060 restraints weight = 28475.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.044603 restraints weight = 23856.341| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 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 = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.235 14894 Z= 0.268 Angle : 1.586 50.582 20464 Z= 0.903 Chirality : 0.259 6.361 2457 Planarity : 0.004 0.051 2636 Dihedral : 4.437 31.412 2203 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 2066 helix: 1.68 (0.19), residues: 773 sheet: -0.34 (0.33), residues: 220 loop : -1.62 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1057 TYR 0.016 0.001 TYR A 387 PHE 0.016 0.001 PHE E 45 TRP 0.013 0.001 TRP A 199 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00736 (14890) covalent geometry : angle 1.39936 (20452) hydrogen bonds : bond 0.03229 ( 664) hydrogen bonds : angle 4.31300 ( 1918) metal coordination : bond 0.02291 ( 4) metal coordination : angle 30.81822 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.86 seconds wall clock time: 41 minutes 12.63 seconds (2472.63 seconds total)