Starting phenix.real_space_refine on Mon May 19 13:26:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tlt_41372/05_2025/8tlt_41372.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tlt_41372/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tlt_41372/05_2025/8tlt_41372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tlt_41372/05_2025/8tlt_41372.map" model { file = "/net/cci-nas-00/data/ceres_data/8tlt_41372/05_2025/8tlt_41372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tlt_41372/05_2025/8tlt_41372.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 22, 'ARG:plan': 22, 'TYR:plan': 1, 'ASN:plan1': 16, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 60, 'ASP:plan': 49} 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: {'GLN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 11, 'ASP:plan': 5} 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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} 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: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 20, 'GLU:plan': 18, 'ARG:plan': 4} 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: {'GLN:plan1': 3, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 9} 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: {'GLN:plan1': 5, 'HIS:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} 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: 11.64, per 1000 atoms: 0.62 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: 4.63 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 7.37 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: 8.59 Time building geometry restraints manager: 5.35 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: 2.130 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: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 54.840 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 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:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.670 ------------------------------------------------------------------------------- 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 : 4.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (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 TRP 0.010 0.001 TRP A 155 HIS 0.004 0.001 HIS D 51 PHE 0.016 0.001 PHE A 528 TYR 0.014 0.001 TYR A 880 ARG 0.004 0.000 ARG A1435 Details of bonding type rmsd hydrogen bonds : bond 0.15887 ( 866) hydrogen bonds : angle 6.45378 ( 2469) metal coordination : bond 0.00329 ( 4) metal coordination : angle 11.66180 ( 12) covalent geometry : bond 0.00473 (18675) covalent geometry : angle 0.67046 (25517) *********************** 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 : 2.210 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: 0.7272 time to fit residues: 216.0985 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 : 1.998 ------------------------------------------------------------------------------- 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 200 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 886 GLN A 895 GLN A 901 ASN A1300 HIS A1348 ASN D 41 ASN D 214 GLN E 38 GLN ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 HIS B 863 ASN B 939 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.101730 restraints weight = 20278.410| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.53 r_work: 0.3053 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.250 18679 Z= 0.361 Angle : 1.482 50.649 25529 Z= 0.842 Chirality : 0.237 6.422 2989 Planarity : 0.005 0.050 3094 Dihedral : 11.157 79.311 2835 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.21 % Favored : 94.75 % Rotamer: Outliers : 4.52 % Allowed : 18.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2341 helix: 1.38 (0.17), residues: 909 sheet: -0.29 (0.29), residues: 294 loop : -1.02 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 604 HIS 0.009 0.002 HIS B 925 PHE 0.023 0.002 PHE E 215 TYR 0.021 0.002 TYR A 613 ARG 0.006 0.001 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.06023 ( 866) hydrogen bonds : angle 5.15439 ( 2469) metal coordination : bond 0.05776 ( 4) metal coordination : angle 30.62901 ( 12) covalent geometry : bond 0.00956 (18675) covalent geometry : angle 1.32563 (25517) *********************** 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 284 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 217 time to evaluate : 2.209 Fit side-chains REVERT: A 755 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8255 (tp) REVERT: A 1199 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.7277 (m-80) REVERT: E 44 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8678 (pt0) REVERT: E 60 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8329 (tp30) REVERT: E 99 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7112 (mp10) REVERT: F 60 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7509 (ttp-170) REVERT: F 186 GLN cc_start: 0.7941 (tt0) cc_final: 0.7648 (tm-30) outliers start: 67 outliers final: 23 residues processed: 266 average time/residue: 0.7420 time to fit residues: 242.9332 Evaluate side-chains 230 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1207 THR 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 60 GLU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 63 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 ASN D 214 GLN ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** F 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN B 863 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 = 0.3495 r_free = 0.3495 target = 0.131877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105136 restraints weight = 20342.170| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.56 r_work: 0.3116 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1207 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= 0.247 Angle : 1.416 50.438 25529 Z= 0.810 Chirality : 0.236 6.389 2989 Planarity : 0.003 0.044 3094 Dihedral : 10.674 72.656 2829 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 3.17 % Allowed : 19.76 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2341 helix: 1.75 (0.17), residues: 903 sheet: -0.39 (0.28), residues: 302 loop : -0.98 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 155 HIS 0.003 0.001 HIS D 51 PHE 0.013 0.001 PHE E 215 TYR 0.014 0.001 TYR A 880 ARG 0.003 0.000 ARG A1435 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 866) hydrogen bonds : angle 4.80619 ( 2469) metal coordination : bond 0.05669 ( 4) metal coordination : angle 30.59490 ( 12) covalent geometry : bond 0.00687 (18675) covalent geometry : angle 1.25095 (25517) *********************** 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 265 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 2.125 Fit side-chains REVERT: A 755 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8222 (tp) REVERT: E 44 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8612 (pt0) REVERT: E 50 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7361 (mtp180) REVERT: E 60 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8303 (tp30) REVERT: E 99 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.6981 (mp10) REVERT: F 60 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.6965 (ttp-170) REVERT: F 186 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: G 71 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7490 (tt) outliers start: 47 outliers final: 18 residues processed: 255 average time/residue: 0.7255 time to fit residues: 227.4514 Evaluate side-chains 233 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 2.287 ------------------------------------------------------------------------------- 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 973 VAL Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1130 LYS Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 146 ASN 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 5 VAL 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 33 LEU Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 106 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 66 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 108 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 ASN ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 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 = 0.3460 r_free = 0.3460 target = 0.129075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.102386 restraints weight = 20256.419| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.55 r_work: 0.3084 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1437 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= 0.285 Angle : 1.433 50.479 25529 Z= 0.818 Chirality : 0.239 6.495 2989 Planarity : 0.004 0.046 3094 Dihedral : 10.859 73.624 2829 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.21 % Favored : 94.75 % Rotamer: Outliers : 4.18 % Allowed : 18.88 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2341 helix: 1.60 (0.17), residues: 897 sheet: -0.54 (0.28), residues: 311 loop : -1.05 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 155 HIS 0.005 0.001 HIS A 812 PHE 0.016 0.002 PHE E 215 TYR 0.015 0.002 TYR A 880 ARG 0.004 0.000 ARG A1447 Details of bonding type rmsd hydrogen bonds : bond 0.04997 ( 866) hydrogen bonds : angle 4.82248 ( 2469) metal coordination : bond 0.06069 ( 4) metal coordination : angle 30.48142 ( 12) covalent geometry : bond 0.00775 (18675) covalent geometry : angle 1.27175 (25517) *********************** 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 268 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 2.060 Fit side-chains REVERT: A 755 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8226 (tp) REVERT: A 997 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8586 (mtt180) REVERT: A 1199 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.7335 (m-10) REVERT: E 44 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8653 (pt0) REVERT: E 50 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7305 (mtp180) REVERT: E 60 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: E 99 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7105 (mp10) REVERT: F -1 LEU cc_start: 0.6062 (OUTLIER) cc_final: 0.5636 (tm) REVERT: F 60 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7354 (ttp-170) REVERT: F 186 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: G 71 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7516 (tt) outliers start: 62 outliers final: 27 residues processed: 255 average time/residue: 0.7149 time to fit residues: 223.3660 Evaluate side-chains 240 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 1.982 ------------------------------------------------------------------------------- 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 318 MET Chi-restraints excluded: chain A residue 707 LEU 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 1045 THR Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1130 LYS Chi-restraints excluded: chain A residue 1189 ILE 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 5 VAL 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 60 ARG Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 106 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 174 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 HIS ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN B 863 ASN B 939 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103166 restraints weight = 19730.785| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.48 r_work: 0.2988 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 18679 Z= 0.282 Angle : 1.434 50.569 25529 Z= 0.819 Chirality : 0.237 6.400 2989 Planarity : 0.004 0.046 3094 Dihedral : 10.923 73.613 2829 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.83 % Rotamer: Outliers : 3.98 % Allowed : 19.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2341 helix: 1.57 (0.17), residues: 897 sheet: -0.62 (0.28), residues: 311 loop : -1.08 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 155 HIS 0.005 0.001 HIS B 925 PHE 0.016 0.002 PHE A 528 TYR 0.014 0.002 TYR A 880 ARG 0.004 0.000 ARG A1435 Details of bonding type rmsd hydrogen bonds : bond 0.04913 ( 866) hydrogen bonds : angle 4.80507 ( 2469) metal coordination : bond 0.05978 ( 4) metal coordination : angle 30.56620 ( 12) covalent geometry : bond 0.00769 (18675) covalent geometry : angle 1.27216 (25517) *********************** 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 264 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 205 time to evaluate : 2.049 Fit side-chains REVERT: A 755 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8333 (tp) REVERT: A 954 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8365 (pt0) REVERT: A 997 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8602 (mtt180) REVERT: A 1199 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.7501 (m-10) REVERT: E 44 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8660 (pt0) REVERT: E 50 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7311 (mtp180) REVERT: E 60 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: E 99 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: E 227 LEU cc_start: 0.8215 (mt) cc_final: 0.7923 (mp) REVERT: F 60 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7400 (ttp-170) REVERT: F 186 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: G 71 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7394 (tt) outliers start: 59 outliers final: 32 residues processed: 250 average time/residue: 0.7728 time to fit residues: 236.7985 Evaluate side-chains 241 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 2.294 ------------------------------------------------------------------------------- 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 318 MET Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 790 VAL 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 1045 THR Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1130 LYS Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain D residue 39 SER 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 5 VAL 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 29 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 71 LEU 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 164 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 213 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 GLN F 262 ASN F 316 HIS G 103 GLN B 863 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 = 0.3496 r_free = 0.3496 target = 0.132165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.105953 restraints weight = 19830.357| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.48 r_work: 0.3105 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 0.248 18679 Z= 0.237 Angle : 1.409 50.428 25529 Z= 0.807 Chirality : 0.236 6.369 2989 Planarity : 0.003 0.044 3094 Dihedral : 10.555 72.780 2829 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.00 % Rotamer: Outliers : 3.57 % Allowed : 19.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2341 helix: 1.88 (0.17), residues: 895 sheet: -0.61 (0.28), residues: 311 loop : -0.98 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 155 HIS 0.003 0.001 HIS D 51 PHE 0.012 0.001 PHE A 528 TYR 0.014 0.001 TYR A 880 ARG 0.003 0.000 ARG A1435 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 866) hydrogen bonds : angle 4.62490 ( 2469) metal coordination : bond 0.04792 ( 4) metal coordination : angle 30.54187 ( 12) covalent geometry : bond 0.00668 (18675) covalent geometry : angle 1.24428 (25517) *********************** 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 264 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 211 time to evaluate : 1.962 Fit side-chains REVERT: A 112 ILE cc_start: 0.8913 (mm) cc_final: 0.8695 (mm) REVERT: A 755 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8344 (tp) REVERT: A 841 ILE cc_start: 0.8521 (tp) cc_final: 0.8230 (tp) REVERT: A 954 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8359 (pt0) REVERT: A 997 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8627 (mtt180) REVERT: A 1199 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.7385 (m-10) REVERT: E 44 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8644 (pt0) REVERT: E 50 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7343 (mtp180) REVERT: E 60 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: E 99 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7062 (mp10) REVERT: E 227 LEU cc_start: 0.8134 (mt) cc_final: 0.7828 (mp) REVERT: F 60 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.6888 (ttp-170) REVERT: F 186 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7922 (tm-30) outliers start: 53 outliers final: 30 residues processed: 252 average time/residue: 0.7292 time to fit residues: 223.9039 Evaluate side-chains 240 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 1.952 ------------------------------------------------------------------------------- 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 707 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 790 VAL 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 1045 THR Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1130 LYS Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1472 ASP 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 5 VAL 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 29 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 67 ILE 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 123 optimal weight: 0.9990 chunk 44 optimal weight: 0.0470 chunk 146 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 108 optimal weight: 0.0270 chunk 120 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 GLN B 863 ASN B 939 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.108338 restraints weight = 20363.674| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.55 r_work: 0.3161 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.247 18679 Z= 0.227 Angle : 1.399 50.395 25529 Z= 0.801 Chirality : 0.235 6.342 2989 Planarity : 0.003 0.043 3094 Dihedral : 10.118 71.688 2829 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.90 % Allowed : 20.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2341 helix: 2.13 (0.18), residues: 893 sheet: -0.45 (0.29), residues: 290 loop : -0.94 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 155 HIS 0.003 0.001 HIS D 51 PHE 0.014 0.001 PHE A 528 TYR 0.013 0.001 TYR E 16 ARG 0.005 0.000 ARG A1435 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 866) hydrogen bonds : angle 4.42324 ( 2469) metal coordination : bond 0.03651 ( 4) metal coordination : angle 30.56934 ( 12) covalent geometry : bond 0.00645 (18675) covalent geometry : angle 1.23190 (25517) *********************** 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 261 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 2.070 Fit side-chains REVERT: A 841 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8038 (tp) REVERT: A 954 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8337 (pt0) REVERT: A 997 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8548 (mtt180) REVERT: A 1199 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: D 76 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8221 (t) REVERT: E 44 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8635 (pt0) REVERT: E 50 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7220 (mtp180) REVERT: E 60 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: E 227 LEU cc_start: 0.8092 (mt) cc_final: 0.7830 (mp) REVERT: F 186 GLN cc_start: 0.8063 (tt0) cc_final: 0.7788 (tm-30) outliers start: 43 outliers final: 19 residues processed: 252 average time/residue: 0.7447 time to fit residues: 228.8757 Evaluate side-chains 239 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 2.079 ------------------------------------------------------------------------------- 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 600 MET Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 790 VAL 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 1199 PHE Chi-restraints excluded: chain D residue 39 SER 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 29 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 106 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1006 ASN A1502 ASN E 214 GLN F 316 HIS B 939 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.103532 restraints weight = 19822.427| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.47 r_work: 0.3107 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1669 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= 0.289 Angle : 1.433 50.592 25529 Z= 0.818 Chirality : 0.237 6.420 2989 Planarity : 0.004 0.047 3094 Dihedral : 10.729 73.037 2829 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.21 % Favored : 94.75 % Rotamer: Outliers : 3.30 % Allowed : 20.57 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2341 helix: 1.78 (0.17), residues: 898 sheet: -0.59 (0.28), residues: 311 loop : -1.00 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 881 HIS 0.006 0.001 HIS B 925 PHE 0.017 0.002 PHE E 215 TYR 0.017 0.002 TYR A 880 ARG 0.004 0.000 ARG A1435 Details of bonding type rmsd hydrogen bonds : bond 0.04792 ( 866) hydrogen bonds : angle 4.65832 ( 2469) metal coordination : bond 0.05746 ( 4) metal coordination : angle 30.52517 ( 12) covalent geometry : bond 0.00787 (18675) covalent geometry : angle 1.27161 (25517) *********************** 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 249 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 2.172 Fit side-chains REVERT: A 841 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8243 (tp) REVERT: A 954 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8349 (pt0) REVERT: A 997 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8643 (mtt180) REVERT: A 1199 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.7437 (m-10) REVERT: E 44 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8648 (pt0) REVERT: E 50 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7417 (mtp180) REVERT: E 60 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: E 99 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: E 227 LEU cc_start: 0.8214 (mt) cc_final: 0.7883 (mp) REVERT: F 186 GLN cc_start: 0.8356 (tt0) cc_final: 0.8116 (tm-30) outliers start: 49 outliers final: 27 residues processed: 236 average time/residue: 0.8067 time to fit residues: 231.8366 Evaluate side-chains 231 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 2.022 ------------------------------------------------------------------------------- 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 715 MET Chi-restraints excluded: chain A residue 790 VAL 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 1045 THR Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1130 LYS Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain D residue 39 SER 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 29 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 34 SER 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 206 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1502 ASN E 214 GLN G 10 ASN B 939 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103976 restraints weight = 19853.895| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.48 r_work: 0.3007 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 18679 Z= 0.267 Angle : 1.425 50.528 25529 Z= 0.814 Chirality : 0.237 6.396 2989 Planarity : 0.004 0.045 3094 Dihedral : 10.797 73.139 2829 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.17 % Favored : 94.79 % Rotamer: Outliers : 2.83 % Allowed : 21.04 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2341 helix: 1.78 (0.17), residues: 898 sheet: -0.60 (0.28), residues: 311 loop : -1.04 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 881 HIS 0.004 0.001 HIS B 925 PHE 0.019 0.001 PHE A 528 TYR 0.015 0.001 TYR A 880 ARG 0.005 0.000 ARG A1435 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 866) hydrogen bonds : angle 4.64860 ( 2469) metal coordination : bond 0.05287 ( 4) metal coordination : angle 30.54595 ( 12) covalent geometry : bond 0.00735 (18675) covalent geometry : angle 1.26224 (25517) *********************** 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 246 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 2.177 Fit side-chains REVERT: A 112 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8527 (mm) REVERT: A 841 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8222 (tp) REVERT: A 954 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8362 (pt0) REVERT: A 997 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8587 (mtt180) REVERT: A 1199 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.7391 (m-10) REVERT: E 44 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8683 (pt0) REVERT: E 50 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7303 (mtp180) REVERT: E 60 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: E 99 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.6976 (mp10) REVERT: E 227 LEU cc_start: 0.8225 (mt) cc_final: 0.7908 (mp) REVERT: F 86 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6946 (tp) REVERT: F 186 GLN cc_start: 0.8276 (tt0) cc_final: 0.8039 (tm-30) outliers start: 42 outliers final: 27 residues processed: 235 average time/residue: 0.7694 time to fit residues: 221.6052 Evaluate side-chains 236 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE 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 715 MET Chi-restraints excluded: chain A residue 790 VAL 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 1045 THR Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1130 LYS Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 39 SER 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 5 VAL 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 29 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 34 SER 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 216 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 24 optimal weight: 0.0040 chunk 197 optimal weight: 0.6980 chunk 204 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1502 ASN 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 = 0.3499 r_free = 0.3499 target = 0.132411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.106329 restraints weight = 19829.969| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.47 r_work: 0.3033 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1685 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= 0.238 Angle : 1.410 50.476 25529 Z= 0.807 Chirality : 0.236 6.371 2989 Planarity : 0.003 0.043 3094 Dihedral : 10.484 72.945 2829 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 2.76 % Allowed : 21.11 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2341 helix: 2.02 (0.17), residues: 893 sheet: -0.57 (0.28), residues: 311 loop : -0.99 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 155 HIS 0.004 0.001 HIS D 51 PHE 0.018 0.001 PHE A 528 TYR 0.014 0.001 TYR E 16 ARG 0.004 0.000 ARG A1435 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 866) hydrogen bonds : angle 4.52260 ( 2469) metal coordination : bond 0.04200 ( 4) metal coordination : angle 30.57156 ( 12) covalent geometry : bond 0.00670 (18675) covalent geometry : angle 1.24465 (25517) ********************** 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 245 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 2.145 Fit side-chains REVERT: A 755 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8494 (tp) REVERT: A 841 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8140 (tp) REVERT: A 954 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8357 (pt0) REVERT: A 997 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8583 (mtt180) REVERT: A 1199 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.7369 (m-10) REVERT: E 44 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8680 (pt0) REVERT: E 50 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7314 (mtp180) REVERT: E 60 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8366 (tp30) REVERT: E 227 LEU cc_start: 0.8171 (mt) cc_final: 0.7849 (mp) REVERT: F 86 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6942 (tp) REVERT: F 186 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.8019 (tm-30) outliers start: 41 outliers final: 23 residues processed: 235 average time/residue: 0.7433 time to fit residues: 213.6608 Evaluate side-chains 233 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 2.093 ------------------------------------------------------------------------------- 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 715 MET Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 790 VAL 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 1045 THR Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 39 SER 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 29 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 34 SER 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 20 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 112 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 14 optimal weight: 0.0570 chunk 91 optimal weight: 4.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1502 ASN E 214 GLN B 863 ASN B 939 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.106113 restraints weight = 20396.404| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.54 r_work: 0.3132 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1678 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= 0.235 Angle : 1.406 50.381 25529 Z= 0.805 Chirality : 0.236 6.362 2989 Planarity : 0.003 0.044 3094 Dihedral : 10.361 72.984 2829 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.36 % Allowed : 21.58 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2341 helix: 2.09 (0.17), residues: 892 sheet: -0.55 (0.28), residues: 311 loop : -0.95 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 155 HIS 0.003 0.001 HIS D 51 PHE 0.019 0.001 PHE A 528 TYR 0.014 0.001 TYR E 16 ARG 0.005 0.000 ARG A1435 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 866) hydrogen bonds : angle 4.46813 ( 2469) metal coordination : bond 0.04795 ( 4) metal coordination : angle 30.50373 ( 12) covalent geometry : bond 0.00662 (18675) covalent geometry : angle 1.24051 (25517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11312.55 seconds wall clock time: 195 minutes 17.83 seconds (11717.83 seconds total)