Starting phenix.real_space_refine on Sun Aug 24 08:53:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tlt_41372/08_2025/8tlt_41372.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tlt_41372/08_2025/8tlt_41372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tlt_41372/08_2025/8tlt_41372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tlt_41372/08_2025/8tlt_41372.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tlt_41372/08_2025/8tlt_41372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tlt_41372/08_2025/8tlt_41372.map" } resolution = 2.85 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= 0.001 sd= 0.138 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 29 5.49 5 S 83 5.16 5 C 11885 2.51 5 N 3057 2.21 5 O 3585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18644 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 9457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1272, 9457 Classifications: {'peptide': 1272} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PTRANS': 59, 'TRANS': 1212} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 937 Unresolved non-hydrogen angles: 1190 Unresolved non-hydrogen dihedrals: 709 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'ASP:plan': 49, 'ASN:plan1': 16, 'HIS:plan': 3, 'GLU:plan': 60, 'GLN:plan1': 22, 'PHE:plan': 2, 'ARG:plan': 22, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 545 Chain: "D" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1375 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain breaks: 5 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 6, 'ARG:plan': 3, 'GLU:plan': 11, 'GLN:plan1': 3, 'ASP:plan': 5, 'HIS:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "E" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1737 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 7, 'GLN:plan1': 4, 'ASP:plan': 12, 'GLU:plan': 9, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 130 Chain: "F" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3312 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 26, 'TRANS': 430} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 20, 'ASN:plan1': 7, 'GLU:plan': 18, 'ARG:plan': 4, 'GLN:plan1': 7, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 223 Chain: "G" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 871 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 9, 'GLN:plan1': 3, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 884 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 4, 'GLN:plan1': 5, 'ASN:plan1': 6, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "P" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 212 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 322 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 291 Unusual residues: {' CA': 1, 'DCP': 1, 'SF4': 1} Classifications: {'undetermined': 3, 'water': 254} Link IDs: {None: 256} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9218 SG CYS A1473 45.294 84.292 92.082 1.00 41.19 S ATOM 9040 SG CYS A1449 41.411 89.583 92.071 1.00 38.04 S ATOM 9178 SG CYS A1468 47.945 90.409 93.792 1.00 36.28 S ATOM 9018 SG CYS A1446 46.553 89.212 87.658 1.00 36.62 S Time building chain proxies: 4.03, per 1000 atoms: 0.22 Number of scatterers: 18644 At special positions: 0 Unit cell: (85.52, 146.453, 180.661, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 83 16.00 P 29 15.00 O 3585 8.00 N 3057 7.00 C 11885 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: 1.39 Conformation dependent library (CDL) restraints added in 680.2 milliseconds Enol-peptide restraints added in 1.7 microseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1601 " pdb="FE1 SF4 A1601 " - pdb=" SG CYS A1473 " pdb="FE2 SF4 A1601 " - pdb=" SG CYS A1449 " pdb="FE4 SF4 A1601 " - pdb=" SG CYS A1446 " pdb="FE3 SF4 A1601 " - pdb=" SG CYS A1468 " Number of angles added : 12 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 21 sheets defined 40.6% alpha, 14.8% beta 10 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 95 through 117 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 306 through 322 removed outlier: 4.266A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 531 through 540 removed outlier: 4.215A pdb=" N ASN A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 removed outlier: 3.608A pdb=" N ASP A 557 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 559 " --> pdb=" O VAL A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 725 through 735 Processing helix chain 'A' and resid 744 through 760 Processing helix chain 'A' and resid 773 through 784 removed outlier: 3.594A pdb=" N ILE A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 794 removed outlier: 3.511A pdb=" N GLU A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 813 Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 840 through 850 Processing helix chain 'A' and resid 857 through 866 Processing helix chain 'A' and resid 870 through 896 Processing helix chain 'A' and resid 896 through 909 Processing helix chain 'A' and resid 911 through 918 removed outlier: 3.654A pdb=" N VAL A 915 " --> pdb=" O ASP A 911 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR A 916 " --> pdb=" O PHE A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 933 removed outlier: 3.916A pdb=" N LYS A 923 " --> pdb=" O GLY A 919 " (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 1018 through 1023 Processing helix chain 'A' and resid 1044 through 1067 removed outlier: 3.723A pdb=" N ILE A1067 " --> pdb=" O THR A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1094 Processing helix chain 'A' and resid 1106 through 1131 removed outlier: 3.668A pdb=" N ASP A1131 " --> pdb=" O ILE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1172 removed outlier: 4.217A pdb=" N SER A1160 " --> pdb=" O ILE A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1241 Processing helix chain 'A' and resid 1243 through 1261 removed outlier: 3.809A pdb=" N ILE A1247 " --> pdb=" O ASP A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1299 removed outlier: 3.518A pdb=" N VAL A1291 " --> pdb=" O ALA A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1327 removed outlier: 3.763A pdb=" N ARG A1326 " --> pdb=" O LEU A1322 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS A1327 " --> pdb=" O LEU A1323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1322 through 1327' Processing helix chain 'A' and resid 1329 through 1336 Processing helix chain 'A' and resid 1342 through 1350 Processing helix chain 'A' and resid 1351 through 1360 Processing helix chain 'A' and resid 1365 through 1373 removed outlier: 4.311A pdb=" N TRP A1369 " --> pdb=" O ASN A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1420 Processing helix chain 'A' and resid 1420 through 1455 removed outlier: 4.252A pdb=" N ARG A1452 " --> pdb=" O THR A1448 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR A1453 " --> pdb=" O CYS A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1467 Processing helix chain 'A' and resid 1473 through 1487 removed outlier: 3.694A pdb=" N TYR A1477 " --> pdb=" O CYS A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1502 Processing helix chain 'D' and resid 2 through 24 removed outlier: 4.109A pdb=" N VAL D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 68 Processing helix chain 'D' and resid 109 through 131 removed outlier: 3.644A pdb=" N VAL D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 131 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 removed outlier: 4.147A pdb=" N SER D 243 " --> pdb=" O ILE D 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 24 removed outlier: 3.922A pdb=" N LYS E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 68 removed outlier: 3.617A pdb=" N LYS E 68 " --> pdb=" O ASP E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 131 removed outlier: 3.805A pdb=" N LYS E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU E 131 " --> pdb=" O HIS E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 175 removed outlier: 3.598A pdb=" N SER E 175 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 0 through 9 Processing helix chain 'F' and resid 52 through 76 removed outlier: 4.089A pdb=" N ILE F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 96 removed outlier: 4.098A 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 131 through 137 Processing helix chain 'F' and resid 161 through 165 removed outlier: 3.531A pdb=" N SER F 164 " --> pdb=" O PHE F 161 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR F 165 " --> pdb=" O ILE F 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 161 through 165' Processing helix chain 'F' and resid 226 through 241 removed outlier: 4.399A pdb=" N LEU F 230 " --> pdb=" O SER F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 252 Processing helix chain 'F' and resid 267 through 271 removed outlier: 4.194A pdb=" N VAL F 271 " --> pdb=" O ILE F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 291 removed outlier: 3.663A pdb=" N LEU F 276 " --> pdb=" O ASN F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 325 Processing helix chain 'F' and resid 357 through 364 Processing helix chain 'F' and resid 391 through 405 Processing helix chain 'F' and resid 411 through 416 Processing helix chain 'G' and resid 4 through 15 Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 32 through 45 Processing helix chain 'G' and resid 76 through 78 No H-bonds generated for 'chain 'G' and resid 76 through 78' Processing helix chain 'B' and resid 882 through 897 Processing helix chain 'B' and resid 904 through 921 Processing helix chain 'B' and resid 923 through 941 Processing helix chain 'B' and resid 950 through 961 Processing helix chain 'B' and resid 963 through 968 removed outlier: 3.633A pdb=" N ARG B 968 " --> pdb=" O LEU B 965 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 35 removed outlier: 6.808A pdb=" N GLN A 70 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE A 268 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU A 72 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE A 270 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N HIS A 74 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 188 through 189 removed outlier: 7.498A pdb=" N ILE A 938 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 146 " --> pdb=" O ILE A 938 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 177 through 179 removed outlier: 5.634A pdb=" N ALA D 143 " --> pdb=" O TYR A 523 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG D 74 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN D 81 " --> pdb=" O CYS D 87 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS D 87 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN D 214 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 563 through 565 removed outlier: 4.014A pdb=" N TYR A 563 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=AA7, first strand: chain 'E' and resid 178 through 180 removed outlier: 4.457A pdb=" N SER A 603 " --> pdb=" O CYS E 180 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG E 74 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN E 81 " --> pdb=" O CYS E 87 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N CYS E 87 " --> pdb=" O ASN E 81 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN E 214 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE E 197 " --> pdb=" O ASP B 982 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 739 through 742 removed outlier: 7.089A pdb=" N SER A 692 " --> pdb=" O VAL A 717 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N HIS A 675 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE A 694 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU A 673 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TRP A 696 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR A 671 " --> pdb=" O TRP A 696 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU A 698 " --> pdb=" O HIS A 669 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N HIS A 669 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU A 670 " --> pdb=" O SER A 765 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 965 through 967 Processing sheet with id=AB1, first strand: chain 'A' and resid 1137 through 1140 removed outlier: 6.173A pdb=" N VAL A1138 " --> pdb=" O TYR A1149 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR A1149 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR A1140 " --> pdb=" O PHE A1147 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR A1185 " --> pdb=" O TYR A1201 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N TYR A1201 " --> pdb=" O TYR A1185 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ARG A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 994 through 997 removed outlier: 6.607A pdb=" N MET A 994 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA A1037 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 996 " --> pdb=" O VAL A1035 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1006 through 1008 removed outlier: 3.617A pdb=" N SER A1011 " --> pdb=" O LEU A1008 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1270 through 1274 removed outlier: 4.132A pdb=" N LYS A1272 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A1308 " --> 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 'E' and resid 32 through 37 removed outlier: 9.253A pdb=" N PHE E 32 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N VAL E 46 " --> pdb=" O PHE E 32 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N TYR E 34 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N GLN E 44 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR E 36 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 23 through 24 removed outlier: 5.881A pdb=" N ARG F 23 " --> pdb=" O LYS G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 88 through 89 removed outlier: 6.732A pdb=" N LEU F 88 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N VAL F 105 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE F 146 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N PHE F 185 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU F 156 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 88 through 89 removed outlier: 6.732A pdb=" N LEU F 88 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N VAL F 105 " --> pdb=" O LEU F 88 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AC2, first strand: chain 'F' and resid 336 through 338 removed outlier: 4.138A pdb=" N SER F 295 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS F 213 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LEU F 258 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA F 215 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR G 64 " --> pdb=" O TYR G 60 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR G 60 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE G 57 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE G 85 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N CYS G 59 " --> pdb=" O CYS G 83 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N CYS G 83 " --> pdb=" O CYS G 59 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 343 through 347 removed outlier: 6.812A pdb=" N ASP F 351 " --> pdb=" O VAL F 435 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE F 437 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU F 353 " --> pdb=" O ILE F 437 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA F 439 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL F 355 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLN F 441 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY F 445 " --> pdb=" O SER F 460 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2415 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 7578 1.40 - 1.59: 10927 1.59 - 1.77: 53 1.77 - 1.96: 105 1.96 - 2.14: 12 Bond restraints: 18675 Sorted by residual: bond pdb=" S1 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.103 0.177 3.00e-02 1.11e+03 3.46e+01 bond pdb=" S4 SF4 A1601 " pdb="FE2 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.123 0.157 3.00e-02 1.11e+03 2.72e+01 bond pdb=" S2 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.124 0.156 3.00e-02 1.11e+03 2.71e+01 bond pdb=" S3 SF4 A1601 " pdb="FE2 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.124 0.156 3.00e-02 1.11e+03 2.70e+01 bond pdb=" S4 SF4 A1601 " pdb="FE1 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.124 0.156 3.00e-02 1.11e+03 2.70e+01 ... (remaining 18670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 25449 3.38 - 6.76: 43 6.76 - 10.14: 1 10.14 - 13.53: 0 13.53 - 16.91: 24 Bond angle restraints: 25517 Sorted by residual: angle pdb="FE3 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.61 -16.91 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 90.44 -16.74 1.50e+00 4.44e-01 1.24e+02 angle pdb="FE1 SF4 A1601 " pdb=" S2 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.39 -16.69 1.50e+00 4.44e-01 1.24e+02 angle pdb="FE1 SF4 A1601 " pdb=" S3 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.38 -16.68 1.50e+00 4.44e-01 1.24e+02 angle pdb="FE1 SF4 A1601 " pdb=" S4 SF4 A1601 " pdb="FE3 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.34 -16.64 1.50e+00 4.44e-01 1.23e+02 ... (remaining 25512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 9541 17.84 - 35.68: 1030 35.68 - 53.52: 345 53.52 - 71.36: 80 71.36 - 89.20: 14 Dihedral angle restraints: 11010 sinusoidal: 3977 harmonic: 7033 Sorted by residual: dihedral pdb=" CA TYR A1095 " pdb=" C TYR A1095 " pdb=" N THR A1096 " pdb=" CA THR A1096 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ASP A1108 " pdb=" CB ASP A1108 " pdb=" CG ASP A1108 " pdb=" OD1 ASP A1108 " ideal model delta sinusoidal sigma weight residual -30.00 -85.88 55.88 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU E 6 " pdb=" CG GLU E 6 " pdb=" CD GLU E 6 " pdb=" OE1 GLU E 6 " ideal model delta sinusoidal sigma weight residual 0.00 89.20 -89.20 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 11007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.046: 2985 4.046 - 8.093: 0 8.093 - 12.139: 0 12.139 - 16.186: 0 16.186 - 20.232: 4 Chirality restraints: 2989 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 -20.23 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 9.59 -20.15 2.00e-01 2.50e+01 1.01e+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 -9.58 20.14 2.00e-01 2.50e+01 1.01e+04 ... (remaining 2986 not shown) Planarity restraints: 3094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A1348 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C ASN A1348 " 0.035 2.00e-02 2.50e+03 pdb=" O ASN A1348 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A1349 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1346 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C TYR A1346 " -0.030 2.00e-02 2.50e+03 pdb=" O TYR A1346 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A1347 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1352 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A1353 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A1353 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1353 " 0.023 5.00e-02 4.00e+02 ... (remaining 3091 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2333 2.75 - 3.29: 17035 3.29 - 3.83: 31145 3.83 - 4.36: 36697 4.36 - 4.90: 64927 Nonbonded interactions: 152137 Sorted by model distance: nonbonded pdb=" OD2 ASP A1144 " pdb="CA CA A1602 " model vdw 2.216 2.510 nonbonded pdb=" O HIS A1186 " pdb=" O HOH A1701 " model vdw 2.229 3.040 nonbonded pdb=" OD1 ASN G 10 " pdb=" OH TYR G 43 " model vdw 2.251 3.040 nonbonded pdb="CA CA A1602 " pdb=" O2G DCP A1603 " model vdw 2.262 2.510 nonbonded pdb=" O GLY F 128 " pdb=" O HOH F 501 " model vdw 2.263 3.040 ... (remaining 152132 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.840 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 0.177 18679 Z= 0.177 Angle : 0.716 18.431 25529 Z= 0.406 Chirality : 0.738 20.232 2989 Planarity : 0.003 0.042 3094 Dihedral : 17.326 89.197 6434 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.54 % Allowed : 23.60 % Favored : 75.86 % 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 aren not related in a simple way. whole: 0.75 (0.17), residues: 2341 helix: 2.15 (0.17), residues: 886 sheet: 0.27 (0.29), residues: 300 loop : -0.77 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1435 TYR 0.014 0.001 TYR A 880 PHE 0.016 0.001 PHE A 528 TRP 0.010 0.001 TRP A 155 HIS 0.004 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00473 (18675) covalent geometry : angle 0.67046 (25517) hydrogen bonds : bond 0.15887 ( 866) hydrogen bonds : angle 6.45378 ( 2469) metal coordination : bond 0.00329 ( 4) metal coordination : angle 11.66180 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 232 time to evaluate : 0.530 Fit side-chains REVERT: A 354 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7652 (mttp) outliers start: 8 outliers final: 4 residues processed: 240 average time/residue: 0.2978 time to fit residues: 87.0166 Evaluate side-chains 225 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 221 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 ARG Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 449 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.0770 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 9.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 895 GLN A1348 ASN D 41 ASN E 38 GLN ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 HIS B 939 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.138205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113779 restraints weight = 20331.611| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.34 r_work: 0.3217 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.250 18679 Z= 0.232 Angle : 1.406 50.409 25529 Z= 0.804 Chirality : 0.235 6.341 2989 Planarity : 0.003 0.042 3094 Dihedral : 10.013 71.682 2835 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.56 % Allowed : 20.77 % Favored : 76.67 % 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 aren not related in a simple way. whole: 0.83 (0.18), residues: 2341 helix: 2.26 (0.18), residues: 903 sheet: -0.01 (0.28), residues: 311 loop : -0.72 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1435 TYR 0.014 0.001 TYR A 880 PHE 0.014 0.001 PHE E 215 TRP 0.009 0.001 TRP A 155 HIS 0.004 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00655 (18675) covalent geometry : angle 1.23675 (25517) hydrogen bonds : bond 0.04025 ( 866) hydrogen bonds : angle 4.92569 ( 2469) metal coordination : bond 0.04138 ( 4) metal coordination : angle 30.90464 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.682 Fit side-chains REVERT: A 584 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8673 (mt0) REVERT: A 755 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8582 (tp) REVERT: A 841 ILE cc_start: 0.8471 (tp) cc_final: 0.8173 (tp) REVERT: E 44 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8386 (pt0) REVERT: E 99 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7290 (mp10) outliers start: 38 outliers final: 14 residues processed: 261 average time/residue: 0.2801 time to fit residues: 90.8892 Evaluate side-chains 242 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 224 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1492 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain G residue 107 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 87 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 170 optimal weight: 0.0470 chunk 151 optimal weight: 1.9990 chunk 15 optimal weight: 0.0060 chunk 159 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 251 ASN D 214 GLN E 214 GLN G 10 ASN B 939 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.110266 restraints weight = 20432.343| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.59 r_work: 0.3204 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.249 18679 Z= 0.231 Angle : 1.401 50.536 25529 Z= 0.802 Chirality : 0.235 6.377 2989 Planarity : 0.003 0.041 3094 Dihedral : 10.014 71.170 2828 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.97 % Allowed : 20.57 % Favored : 76.47 % 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 aren not related in a simple way. whole: 0.77 (0.18), residues: 2341 helix: 2.29 (0.18), residues: 897 sheet: -0.26 (0.28), residues: 311 loop : -0.75 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1435 TYR 0.014 0.001 TYR A 880 PHE 0.013 0.001 PHE E 215 TRP 0.008 0.001 TRP A 155 HIS 0.003 0.001 HIS A 812 Details of bonding type rmsd covalent geometry : bond 0.00653 (18675) covalent geometry : angle 1.23256 (25517) hydrogen bonds : bond 0.03841 ( 866) hydrogen bonds : angle 4.61643 ( 2469) metal coordination : bond 0.04431 ( 4) metal coordination : angle 30.71794 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 0.573 Fit side-chains REVERT: A 755 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8549 (tp) REVERT: A 841 ILE cc_start: 0.8438 (tp) cc_final: 0.8109 (tp) REVERT: E 44 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8446 (pt0) REVERT: E 99 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7288 (mp10) REVERT: E 227 LEU cc_start: 0.7953 (mt) cc_final: 0.7744 (mp) REVERT: F -1 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5381 (tp) outliers start: 44 outliers final: 17 residues processed: 267 average time/residue: 0.3263 time to fit residues: 106.0702 Evaluate side-chains 246 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1156 ILE Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain F residue -1 LEU Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 159 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A1006 ASN D 214 GLN E 214 GLN F 441 GLN B 939 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112587 restraints weight = 20442.657| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.42 r_work: 0.3205 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.248 18679 Z= 0.229 Angle : 1.398 50.384 25529 Z= 0.800 Chirality : 0.235 6.364 2989 Planarity : 0.003 0.041 3094 Dihedral : 10.009 70.729 2828 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.29 % Allowed : 20.97 % Favored : 76.74 % 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 aren not related in a simple way. whole: 0.78 (0.18), residues: 2341 helix: 2.34 (0.18), residues: 894 sheet: -0.32 (0.28), residues: 311 loop : -0.73 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1435 TYR 0.014 0.001 TYR A 880 PHE 0.012 0.001 PHE E 215 TRP 0.009 0.001 TRP A 155 HIS 0.002 0.001 HIS B 925 Details of bonding type rmsd covalent geometry : bond 0.00650 (18675) covalent geometry : angle 1.22998 (25517) hydrogen bonds : bond 0.03667 ( 866) hydrogen bonds : angle 4.49010 ( 2469) metal coordination : bond 0.04502 ( 4) metal coordination : angle 30.63840 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.743 Fit side-chains REVERT: A 841 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8091 (tp) REVERT: A 997 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8540 (mtt180) REVERT: E 44 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8432 (pt0) REVERT: F -1 LEU cc_start: 0.5871 (OUTLIER) cc_final: 0.5492 (tp) REVERT: F 43 CYS cc_start: 0.7649 (t) cc_final: 0.7304 (t) REVERT: F 344 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8362 (mm-30) outliers start: 34 outliers final: 15 residues processed: 254 average time/residue: 0.3255 time to fit residues: 101.5536 Evaluate side-chains 239 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 1156 ILE Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain F residue -1 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 344 GLU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain G residue 107 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 105 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 225 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 222 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 771 ASN A 886 GLN A 901 ASN D 214 GLN E 214 GLN B 863 ASN B 939 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.105974 restraints weight = 20107.866| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.55 r_work: 0.3131 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 18679 Z= 0.257 Angle : 1.418 50.545 25529 Z= 0.810 Chirality : 0.236 6.400 2989 Planarity : 0.003 0.044 3094 Dihedral : 10.432 71.178 2828 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 3.51 % Allowed : 19.69 % Favored : 76.80 % 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 aren not related in a simple way. whole: 0.55 (0.17), residues: 2341 helix: 2.10 (0.17), residues: 896 sheet: -0.37 (0.28), residues: 310 loop : -0.85 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1435 TYR 0.017 0.001 TYR A 880 PHE 0.014 0.001 PHE E 215 TRP 0.009 0.001 TRP A 155 HIS 0.005 0.001 HIS B 925 Details of bonding type rmsd covalent geometry : bond 0.00713 (18675) covalent geometry : angle 1.25334 (25517) hydrogen bonds : bond 0.04403 ( 866) hydrogen bonds : angle 4.58825 ( 2469) metal coordination : bond 0.05439 ( 4) metal coordination : angle 30.59314 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 0.774 Fit side-chains REVERT: A 755 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8352 (tp) REVERT: A 841 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8070 (tp) REVERT: A 997 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8674 (mtt180) REVERT: A 1199 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.7055 (m-10) REVERT: E 44 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8530 (pt0) REVERT: E 60 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8254 (tp30) REVERT: E 99 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7181 (mp10) REVERT: F 43 CYS cc_start: 0.7807 (t) cc_final: 0.7396 (t) outliers start: 52 outliers final: 20 residues processed: 261 average time/residue: 0.3561 time to fit residues: 112.9122 Evaluate side-chains 234 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 106 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 104 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 182 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN D 214 GLN E 214 GLN B 863 ASN B 939 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.135340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.108608 restraints weight = 20273.814| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.56 r_work: 0.3165 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.248 18679 Z= 0.230 Angle : 1.400 50.386 25529 Z= 0.802 Chirality : 0.236 6.359 2989 Planarity : 0.003 0.042 3094 Dihedral : 10.210 70.405 2828 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 2.49 % Allowed : 21.17 % Favored : 76.33 % 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 aren not related in a simple way. whole: 0.65 (0.17), residues: 2341 helix: 2.25 (0.17), residues: 895 sheet: -0.46 (0.28), residues: 311 loop : -0.81 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1435 TYR 0.014 0.001 TYR A 880 PHE 0.014 0.001 PHE A 528 TRP 0.011 0.001 TRP A 155 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00651 (18675) covalent geometry : angle 1.23298 (25517) hydrogen bonds : bond 0.03741 ( 866) hydrogen bonds : angle 4.45757 ( 2469) metal coordination : bond 0.04349 ( 4) metal coordination : angle 30.57589 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.791 Fit side-chains REVERT: A 755 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8296 (tp) REVERT: A 841 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8028 (tp) REVERT: A 997 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8509 (mtt180) REVERT: A 1199 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.7065 (m-10) REVERT: D 38 GLN cc_start: 0.8581 (pt0) cc_final: 0.8332 (pt0) REVERT: E 44 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8492 (pt0) REVERT: E 50 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7272 (mtp180) REVERT: E 60 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8255 (tp30) REVERT: F 43 CYS cc_start: 0.7835 (t) cc_final: 0.7429 (t) outliers start: 37 outliers final: 15 residues processed: 252 average time/residue: 0.3547 time to fit residues: 109.1271 Evaluate side-chains 240 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 160 optimal weight: 5.9990 chunk 139 optimal weight: 0.0980 chunk 151 optimal weight: 0.6980 chunk 201 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 GLN E 214 GLN B 939 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.134566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.107772 restraints weight = 20321.566| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.57 r_work: 0.3153 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 18679 Z= 0.235 Angle : 1.403 50.478 25529 Z= 0.803 Chirality : 0.236 6.370 2989 Planarity : 0.003 0.043 3094 Dihedral : 10.191 70.355 2828 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.74 % Favored : 95.22 % Rotamer: Outliers : 2.56 % Allowed : 21.24 % Favored : 76.20 % 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 aren not related in a simple way. whole: 0.61 (0.17), residues: 2341 helix: 2.20 (0.17), residues: 897 sheet: -0.49 (0.28), residues: 311 loop : -0.82 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1435 TYR 0.015 0.001 TYR D 27 PHE 0.016 0.001 PHE A 528 TRP 0.009 0.001 TRP A 155 HIS 0.004 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00665 (18675) covalent geometry : angle 1.23684 (25517) hydrogen bonds : bond 0.03835 ( 866) hydrogen bonds : angle 4.43684 ( 2469) metal coordination : bond 0.04405 ( 4) metal coordination : angle 30.57344 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 0.733 Fit side-chains REVERT: A 755 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8302 (tp) REVERT: A 841 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8005 (tp) REVERT: A 997 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8511 (mtt180) REVERT: A 1199 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.7089 (m-10) REVERT: D 38 GLN cc_start: 0.8632 (pt0) cc_final: 0.8389 (pt0) REVERT: E 44 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8503 (pt0) REVERT: E 50 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7270 (mtp180) REVERT: E 60 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8274 (tp30) outliers start: 38 outliers final: 17 residues processed: 252 average time/residue: 0.3551 time to fit residues: 109.5787 Evaluate side-chains 238 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 153 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 37 optimal weight: 0.0770 chunk 131 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 163 optimal weight: 0.2980 chunk 105 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 overall best weight: 1.8744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1006 ASN D 214 GLN E 214 GLN G 103 GLN B 939 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104667 restraints weight = 20179.865| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.55 r_work: 0.3092 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.248 18679 Z= 0.276 Angle : 1.429 50.566 25529 Z= 0.816 Chirality : 0.237 6.408 2989 Planarity : 0.004 0.046 3094 Dihedral : 10.706 71.080 2828 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 2.97 % Allowed : 21.04 % Favored : 75.99 % 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 aren not related in a simple way. whole: 0.35 (0.17), residues: 2341 helix: 1.93 (0.17), residues: 891 sheet: -0.58 (0.28), residues: 312 loop : -0.93 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1435 TYR 0.016 0.002 TYR A 880 PHE 0.019 0.002 PHE A 528 TRP 0.010 0.001 TRP A1134 HIS 0.005 0.001 HIS B 925 Details of bonding type rmsd covalent geometry : bond 0.00758 (18675) covalent geometry : angle 1.26662 (25517) hydrogen bonds : bond 0.04726 ( 866) hydrogen bonds : angle 4.65209 ( 2469) metal coordination : bond 0.05827 ( 4) metal coordination : angle 30.54070 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.753 Fit side-chains REVERT: A 755 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8319 (tp) REVERT: A 841 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8155 (tp) REVERT: A 997 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8612 (mtt180) REVERT: A 1065 ASN cc_start: 0.7414 (m110) cc_final: 0.7159 (m110) REVERT: A 1199 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.7271 (m-10) REVERT: D 38 GLN cc_start: 0.8699 (pt0) cc_final: 0.8470 (pt0) REVERT: E 44 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8615 (pt0) REVERT: E 50 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7349 (mtp180) REVERT: E 60 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8304 (tp30) REVERT: E 99 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7170 (mp10) REVERT: F -1 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.5845 (tm) REVERT: F 186 GLN cc_start: 0.8008 (tt0) cc_final: 0.7772 (tm-30) outliers start: 44 outliers final: 20 residues processed: 245 average time/residue: 0.3619 time to fit residues: 108.2369 Evaluate side-chains 233 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain F residue -1 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 106 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 68 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 196 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 202 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 218 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 HIS A1300 HIS D 214 GLN E 214 GLN F 316 HIS B 863 ASN B 939 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.106383 restraints weight = 19933.013| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.29 r_work: 0.2983 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 18679 Z= 0.292 Angle : 1.440 50.573 25529 Z= 0.821 Chirality : 0.237 6.421 2989 Planarity : 0.004 0.047 3094 Dihedral : 10.950 73.134 2828 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.34 % Favored : 94.62 % Rotamer: Outliers : 2.83 % Allowed : 20.77 % Favored : 76.40 % 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 aren not related in a simple way. whole: 0.11 (0.17), residues: 2341 helix: 1.68 (0.17), residues: 898 sheet: -0.65 (0.28), residues: 311 loop : -1.05 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1435 TYR 0.014 0.002 TYR A 880 PHE 0.021 0.002 PHE A 528 TRP 0.012 0.002 TRP A1134 HIS 0.006 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00791 (18675) covalent geometry : angle 1.27900 (25517) hydrogen bonds : bond 0.04967 ( 866) hydrogen bonds : angle 4.75488 ( 2469) metal coordination : bond 0.06197 ( 4) metal coordination : angle 30.52096 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 0.733 Fit side-chains REVERT: A 188 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8809 (mt) REVERT: A 755 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8418 (tp) REVERT: A 954 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8284 (pt0) REVERT: A 997 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8558 (mtt180) REVERT: A 1199 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.7493 (m-10) REVERT: D 38 GLN cc_start: 0.8705 (pt0) cc_final: 0.8494 (pt0) REVERT: E 44 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8661 (pt0) REVERT: E 50 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7285 (mtp180) REVERT: E 60 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8227 (tp30) REVERT: E 99 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.6913 (mp10) REVERT: F -1 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.5884 (tm) REVERT: F 186 GLN cc_start: 0.8206 (tt0) cc_final: 0.7972 (tm-30) outliers start: 42 outliers final: 22 residues processed: 242 average time/residue: 0.3667 time to fit residues: 107.1375 Evaluate side-chains 233 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain F residue -1 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 106 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 91 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 160 optimal weight: 0.3980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 GLN E 214 GLN B 939 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.134082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.111337 restraints weight = 20000.016| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.18 r_work: 0.3082 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 18679 Z= 0.233 Angle : 1.407 50.494 25529 Z= 0.805 Chirality : 0.236 6.387 2989 Planarity : 0.003 0.043 3094 Dihedral : 10.454 70.832 2828 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.53 % Favored : 95.43 % Rotamer: Outliers : 2.36 % Allowed : 21.17 % Favored : 76.47 % 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 aren not related in a simple way. whole: 0.40 (0.17), residues: 2341 helix: 2.07 (0.17), residues: 891 sheet: -0.59 (0.28), residues: 310 loop : -0.98 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1435 TYR 0.013 0.001 TYR E 16 PHE 0.020 0.001 PHE A 528 TRP 0.013 0.001 TRP A 155 HIS 0.005 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00658 (18675) covalent geometry : angle 1.24220 (25517) hydrogen bonds : bond 0.03896 ( 866) hydrogen bonds : angle 4.52853 ( 2469) metal coordination : bond 0.04511 ( 4) metal coordination : angle 30.48584 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.752 Fit side-chains REVERT: A 841 ILE cc_start: 0.8520 (tp) cc_final: 0.8189 (tp) REVERT: A 997 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8615 (mtt180) REVERT: A 1199 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.7351 (m-10) REVERT: E 44 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8564 (pt0) REVERT: E 50 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7396 (mtp180) REVERT: E 60 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8340 (tp30) REVERT: F 186 GLN cc_start: 0.8251 (tt0) cc_final: 0.8030 (tm-30) outliers start: 35 outliers final: 18 residues processed: 244 average time/residue: 0.3759 time to fit residues: 110.9763 Evaluate side-chains 235 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 106 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 133 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1502 ASN D 84 ASN D 214 GLN E 214 GLN F 316 HIS B 863 ASN B 939 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.106023 restraints weight = 19823.381| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.49 r_work: 0.3092 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 18679 Z= 0.250 Angle : 1.414 50.455 25529 Z= 0.809 Chirality : 0.236 6.390 2989 Planarity : 0.003 0.045 3094 Dihedral : 10.510 71.181 2828 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 1.75 % Allowed : 21.92 % Favored : 76.33 % 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 aren not related in a simple way. whole: 0.37 (0.17), residues: 2341 helix: 2.04 (0.17), residues: 890 sheet: -0.59 (0.28), residues: 310 loop : -0.99 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1435 TYR 0.014 0.001 TYR A 880 PHE 0.022 0.001 PHE A 528 TRP 0.010 0.001 TRP A1134 HIS 0.004 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00696 (18675) covalent geometry : angle 1.25027 (25517) hydrogen bonds : bond 0.04212 ( 866) hydrogen bonds : angle 4.55363 ( 2469) metal coordination : bond 0.05260 ( 4) metal coordination : angle 30.48969 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5255.28 seconds wall clock time: 90 minutes 28.98 seconds (5428.98 seconds total)