Starting phenix.real_space_refine on Mon Oct 14 18:25:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlt_41372/10_2024/8tlt_41372.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlt_41372/10_2024/8tlt_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlt_41372/10_2024/8tlt_41372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlt_41372/10_2024/8tlt_41372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlt_41372/10_2024/8tlt_41372.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlt_41372/10_2024/8tlt_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 11.25, per 1000 atoms: 0.60 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: 4.86 Conformation dependent library (CDL) restraints added in 2.5 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: 7.13 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: 9.00 Time building geometry restraints manager: 5.33 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: 0.960 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: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 53.500 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.450 ------------------------------------------------------------------------------- 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 18675 Z= 0.287 Angle : 0.670 16.907 25517 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 232 time to evaluate : 2.143 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: 0.7522 time to fit residues: 221.7133 Evaluate side-chains 225 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 221 time to evaluate : 2.239 ------------------------------------------------------------------------------- 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: 1.9990 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: 3.3990 ------------------------------------------------------------------------------- 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 939 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.259 18675 Z= 0.632 Angle : 1.336 50.712 25517 Z= 0.845 Chirality : 0.235 6.348 2989 Planarity : 0.005 0.051 3094 Dihedral : 11.210 79.702 2835 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.17 % Favored : 94.79 % Rotamer: Outliers : 4.52 % Allowed : 18.61 % Favored : 76.87 % 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: -0.04 (0.17), residues: 2341 helix: 1.31 (0.17), residues: 909 sheet: -0.37 (0.28), residues: 302 loop : -1.04 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 604 HIS 0.009 0.002 HIS B 925 PHE 0.025 0.002 PHE E 215 TYR 0.021 0.002 TYR A 613 ARG 0.006 0.001 ARG D 24 *********************** 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 280 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 213 time to evaluate : 2.196 Fit side-chains REVERT: A 354 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7770 (mttp) REVERT: A 755 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8323 (tp) REVERT: A 1199 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.7161 (m-80) REVERT: E 60 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8036 (tp30) REVERT: E 99 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7055 (mp10) REVERT: F 60 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7265 (ttp-170) REVERT: F 113 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8402 (mttm) REVERT: F 186 GLN cc_start: 0.8055 (tt0) cc_final: 0.7764 (tm-30) outliers start: 67 outliers final: 23 residues processed: 262 average time/residue: 0.8025 time to fit residues: 256.9143 Evaluate side-chains 229 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 199 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 354 LYS 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 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 5 VAL 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 113 LYS 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 120 optimal weight: 0.7980 chunk 67 optimal weight: 0.0980 chunk 179 optimal weight: 3.9990 chunk 147 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 GLN ** E 214 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.247 18675 Z= 0.388 Angle : 1.241 50.519 25517 Z= 0.804 Chirality : 0.236 6.384 2989 Planarity : 0.003 0.043 3094 Dihedral : 10.515 72.195 2829 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 2.90 % Allowed : 19.89 % Favored : 77.21 % 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: 0.35 (0.17), residues: 2341 helix: 1.86 (0.17), residues: 902 sheet: -0.37 (0.28), residues: 303 loop : -0.95 (0.18), 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 0.011 0.001 PHE E 215 TYR 0.013 0.001 TYR A 880 ARG 0.003 0.000 ARG A1435 *********************** 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 268 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 225 time to evaluate : 2.238 Fit side-chains REVERT: A 354 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7741 (mttp) REVERT: A 755 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8275 (tp) REVERT: A 1081 LYS cc_start: 0.7985 (mttm) cc_final: 0.7729 (mttt) REVERT: E 50 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7327 (mtp180) REVERT: E 60 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8020 (tp30) REVERT: E 99 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.6914 (mp10) REVERT: F -1 LEU cc_start: 0.6345 (OUTLIER) cc_final: 0.5860 (tp) REVERT: F 186 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7620 (tm-30) outliers start: 43 outliers final: 16 residues processed: 260 average time/residue: 0.7625 time to fit residues: 243.2732 Evaluate side-chains 232 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 210 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 318 MET 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 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 205 SER 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 E residue 171 ILE Chi-restraints excluded: chain F residue -1 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 107 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 chunk 113 optimal weight: 0.0970 chunk 205 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 GLN ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN B 863 ASN B 939 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.247 18675 Z= 0.574 Angle : 1.304 50.414 25517 Z= 0.830 Chirality : 0.240 6.489 2989 Planarity : 0.004 0.047 3094 Dihedral : 11.181 79.271 2829 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 4.38 % Allowed : 18.68 % 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: -0.11 (0.17), residues: 2341 helix: 1.39 (0.17), residues: 896 sheet: -0.60 (0.28), residues: 312 loop : -1.12 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1134 HIS 0.007 0.001 HIS B 925 PHE 0.020 0.002 PHE E 215 TYR 0.015 0.002 TYR A 839 ARG 0.004 0.001 ARG A1447 *********************** 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 270 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 205 time to evaluate : 2.199 Fit side-chains REVERT: A 354 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7811 (mttp) REVERT: A 755 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8323 (tp) REVERT: A 997 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8535 (mtt180) REVERT: A 1199 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.7381 (m-10) REVERT: E 50 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7295 (mtp180) REVERT: E 60 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: E 99 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7064 (mp10) REVERT: F 43 CYS cc_start: 0.7584 (t) cc_final: 0.7293 (t) REVERT: F 60 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7577 (ttp-170) REVERT: F 186 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: F 191 CYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7748 (t) REVERT: G 71 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7453 (tt) outliers start: 65 outliers final: 29 residues processed: 253 average time/residue: 0.8073 time to fit residues: 248.7494 Evaluate side-chains 241 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 201 time to evaluate : 1.977 ------------------------------------------------------------------------------- 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 354 LYS Chi-restraints excluded: chain A residue 385 THR 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 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 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 E residue 178 VAL 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 191 CYS 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 56 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 191 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 18675 Z= 0.402 Angle : 1.245 50.492 25517 Z= 0.806 Chirality : 0.236 6.378 2989 Planarity : 0.003 0.044 3094 Dihedral : 10.644 72.495 2829 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.53 % Favored : 95.43 % Rotamer: Outliers : 3.30 % Allowed : 19.82 % Favored : 76.87 % 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: 1.82 (0.17), residues: 896 sheet: -0.60 (0.28), residues: 311 loop : -1.03 (0.17), residues: 1134 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 A 528 TYR 0.014 0.001 TYR A 880 ARG 0.004 0.000 ARG A1435 *********************** 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 266 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 217 time to evaluate : 2.236 Fit side-chains REVERT: A 354 LYS cc_start: 0.7980 (ttmt) cc_final: 0.7768 (mttp) REVERT: A 589 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8343 (t) REVERT: A 755 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8290 (tp) REVERT: A 997 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8535 (mtt180) REVERT: A 1081 LYS cc_start: 0.8062 (mttm) cc_final: 0.7811 (mttt) REVERT: A 1199 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.7206 (m-10) REVERT: E 50 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7244 (mtp180) REVERT: E 60 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7314 (tm-30) REVERT: E 99 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.6894 (mp10) REVERT: F 43 CYS cc_start: 0.7564 (t) cc_final: 0.7257 (t) REVERT: F 60 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.6745 (ttp-170) REVERT: F 186 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7841 (tm-30) outliers start: 49 outliers final: 20 residues processed: 257 average time/residue: 0.7800 time to fit residues: 244.7966 Evaluate side-chains 239 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 210 time to evaluate : 2.266 ------------------------------------------------------------------------------- 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 589 THR 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 1172 ASN 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 205 SER 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 106 CYS Chi-restraints excluded: chain G residue 107 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN B 863 ASN B 939 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.247 18675 Z= 0.540 Angle : 1.294 50.579 25517 Z= 0.826 Chirality : 0.238 6.469 2989 Planarity : 0.004 0.048 3094 Dihedral : 11.115 76.037 2829 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.51 % Favored : 94.45 % Rotamer: Outliers : 3.98 % Allowed : 19.49 % Favored : 76.53 % 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: -0.11 (0.17), residues: 2341 helix: 1.46 (0.17), residues: 897 sheet: -0.74 (0.27), residues: 312 loop : -1.14 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1134 HIS 0.007 0.001 HIS B 925 PHE 0.018 0.002 PHE E 215 TYR 0.015 0.002 TYR A 880 ARG 0.004 0.000 ARG A1447 *********************** 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 265 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 206 time to evaluate : 2.440 Fit side-chains REVERT: A 354 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7822 (mttp) REVERT: A 755 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8317 (tp) REVERT: A 954 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7972 (pt0) REVERT: A 997 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8514 (mtt180) REVERT: A 1199 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.7394 (m-10) REVERT: D 59 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7508 (mt-10) REVERT: E 50 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7256 (mtp180) REVERT: E 60 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: E 99 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7079 (mp10) REVERT: F -1 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6392 (tm) REVERT: F 60 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7236 (ttp-170) REVERT: F 186 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7952 (tm-30) REVERT: F 191 CYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7698 (t) REVERT: G 71 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7293 (tt) outliers start: 59 outliers final: 31 residues processed: 249 average time/residue: 0.7982 time to fit residues: 244.0544 Evaluate side-chains 243 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 201 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 1199 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 70 THR 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 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 86 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 191 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 130 optimal weight: 0.1980 chunk 193 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 229 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 B 863 ASN B 939 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 18675 Z= 0.394 Angle : 1.242 50.446 25517 Z= 0.804 Chirality : 0.236 6.367 2989 Planarity : 0.003 0.043 3094 Dihedral : 10.549 72.444 2829 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 2.56 % Allowed : 20.84 % Favored : 76.60 % 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: 0.24 (0.17), residues: 2341 helix: 1.92 (0.18), residues: 892 sheet: -0.68 (0.28), residues: 311 loop : -1.05 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 155 HIS 0.003 0.001 HIS D 51 PHE 0.015 0.001 PHE A 528 TYR 0.014 0.001 TYR E 16 ARG 0.004 0.000 ARG A1435 *********************** 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 253 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 215 time to evaluate : 2.246 Fit side-chains REVERT: A 354 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7743 (mttp) REVERT: A 755 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8281 (tp) REVERT: A 841 ILE cc_start: 0.8116 (tp) cc_final: 0.7825 (tp) REVERT: A 954 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7957 (pt0) REVERT: A 997 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8521 (mtt180) REVERT: A 1081 LYS cc_start: 0.8086 (mttm) cc_final: 0.7835 (mttt) REVERT: A 1199 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.7236 (m-10) REVERT: E 50 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7212 (mtp180) REVERT: E 60 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7406 (tm-30) REVERT: E 99 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.6884 (mp10) REVERT: F 186 GLN cc_start: 0.8091 (tt0) cc_final: 0.7823 (tm-30) REVERT: F 191 CYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7704 (t) REVERT: B 863 ASN cc_start: 0.7396 (m110) cc_final: 0.7158 (m-40) outliers start: 38 outliers final: 22 residues processed: 245 average time/residue: 0.8353 time to fit residues: 251.8948 Evaluate side-chains 237 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 208 time to evaluate : 2.419 ------------------------------------------------------------------------------- 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 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 1156 ILE Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 205 SER 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 61 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.0030 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 GLN B 939 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.246 18675 Z= 0.388 Angle : 1.234 50.453 25517 Z= 0.801 Chirality : 0.235 6.351 2989 Planarity : 0.003 0.043 3094 Dihedral : 10.172 72.459 2829 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 2.56 % Allowed : 20.97 % 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: 0.45 (0.17), residues: 2341 helix: 2.12 (0.18), residues: 894 sheet: -0.59 (0.28), residues: 311 loop : -0.96 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 155 HIS 0.003 0.001 HIS D 51 PHE 0.017 0.001 PHE A 528 TYR 0.013 0.001 TYR E 16 ARG 0.004 0.000 ARG A1435 *********************** 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 258 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 220 time to evaluate : 2.196 Fit side-chains REVERT: A 354 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7682 (mttp) REVERT: A 755 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8335 (tp) REVERT: A 841 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7817 (tp) REVERT: A 954 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7961 (pt0) REVERT: A 997 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8528 (mtt180) REVERT: A 1081 LYS cc_start: 0.8038 (mttm) cc_final: 0.7810 (mttt) REVERT: A 1199 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: E 50 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7179 (mtp180) REVERT: E 60 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: E 99 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.6933 (mp10) REVERT: F 186 GLN cc_start: 0.8086 (tt0) cc_final: 0.7829 (tm-30) REVERT: F 191 CYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7729 (t) outliers start: 38 outliers final: 15 residues processed: 247 average time/residue: 0.8123 time to fit residues: 243.6088 Evaluate side-chains 239 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 216 time to evaluate : 2.292 ------------------------------------------------------------------------------- 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 1045 THR Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain 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 191 CYS 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 208 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 213 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.0570 chunk 167 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- 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 863 ASN B 939 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 18675 Z= 0.403 Angle : 1.242 50.519 25517 Z= 0.804 Chirality : 0.235 6.370 2989 Planarity : 0.003 0.044 3094 Dihedral : 10.286 72.191 2828 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.74 % Favored : 95.22 % Rotamer: Outliers : 2.16 % Allowed : 21.31 % Favored : 76.53 % 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: 2.10 (0.18), residues: 893 sheet: -0.56 (0.28), residues: 311 loop : -0.96 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 881 HIS 0.003 0.001 HIS D 51 PHE 0.017 0.001 PHE A 528 TYR 0.014 0.001 TYR A 880 ARG 0.005 0.000 ARG A1435 *********************** 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 244 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 212 time to evaluate : 2.293 Fit side-chains REVERT: A 354 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7715 (mttp) REVERT: A 584 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8488 (mt0) REVERT: A 755 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8346 (tp) REVERT: A 841 ILE cc_start: 0.8108 (tp) cc_final: 0.7829 (tp) REVERT: A 954 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7965 (pt0) REVERT: A 997 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8508 (mtt180) REVERT: A 1081 LYS cc_start: 0.8042 (mttm) cc_final: 0.7818 (mttt) REVERT: A 1199 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.7109 (m-10) REVERT: E 50 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7191 (mtp180) REVERT: E 60 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: E 99 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7111 (mp10) REVERT: F 186 GLN cc_start: 0.8107 (tt0) cc_final: 0.7836 (tm-30) REVERT: F 191 CYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7679 (t) outliers start: 32 outliers final: 16 residues processed: 238 average time/residue: 0.8415 time to fit residues: 243.5475 Evaluate side-chains 234 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 2.281 ------------------------------------------------------------------------------- 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 584 GLN 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 1199 PHE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain 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 191 CYS 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 226 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 157 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 chunk 218 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 145 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 18675 Z= 0.442 Angle : 1.258 50.390 25517 Z= 0.810 Chirality : 0.237 6.392 2989 Planarity : 0.004 0.046 3094 Dihedral : 10.654 72.968 2828 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.91 % Favored : 95.04 % Rotamer: Outliers : 2.16 % Allowed : 21.38 % 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: 0.32 (0.17), residues: 2341 helix: 1.98 (0.17), residues: 890 sheet: -0.58 (0.28), residues: 311 loop : -1.01 (0.18), residues: 1140 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 0.017 0.001 TYR A 880 ARG 0.005 0.000 ARG A1435 ********************** 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 237 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 2.240 Fit side-chains REVERT: A 354 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7736 (mttp) REVERT: A 584 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8435 (mt0) REVERT: A 755 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8258 (tp) REVERT: A 841 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7886 (tp) REVERT: A 954 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7979 (pt0) REVERT: A 997 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8505 (mtt180) REVERT: A 1199 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.7282 (m-10) REVERT: E 50 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7199 (mtp180) REVERT: E 60 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: E 99 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7082 (mp10) REVERT: F 86 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7376 (tp) REVERT: F 186 GLN cc_start: 0.8122 (tt0) cc_final: 0.7869 (tm-30) REVERT: F 191 CYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7693 (t) REVERT: B 863 ASN cc_start: 0.7393 (m110) cc_final: 0.7154 (m-40) outliers start: 32 outliers final: 18 residues processed: 231 average time/residue: 0.8222 time to fit residues: 231.0432 Evaluate side-chains 230 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 2.155 ------------------------------------------------------------------------------- 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 584 GLN 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 76 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 203 VAL 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 191 CYS Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 106 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 174 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 52 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.132770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.106252 restraints weight = 20532.938| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.57 r_work: 0.3134 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1689 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: