Starting phenix.real_space_refine on Sat Dec 9 04:47:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvp_27012/12_2023/8cvp_27012.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvp_27012/12_2023/8cvp_27012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvp_27012/12_2023/8cvp_27012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvp_27012/12_2023/8cvp_27012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvp_27012/12_2023/8cvp_27012.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvp_27012/12_2023/8cvp_27012.pdb" } resolution = 3.4 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= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 48 5.16 5 C 6340 2.51 5 N 1780 2.21 5 O 1943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 166": "OD1" <-> "OD2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 994": "OE1" <-> "OE2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10112 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 7904 Classifications: {'peptide': 1135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 297} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 39, 'TRANS': 1091} Chain breaks: 1 Unresolved non-hydrogen bonds: 1011 Unresolved non-hydrogen angles: 1287 Unresolved non-hydrogen dihedrals: 813 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 18, 'TYR:plan': 7, 'ASN:plan1': 14, 'TRP:plan': 3, 'HIS:plan': 9, 'PHE:plan': 9, 'GLU:plan': 27, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 536 Chain: "B" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2208 Unusual residues: {' ZN': 1} Classifications: {'peptide': 349, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 330, None: 1} Not linked: pdbres="ASP B 428 " pdbres=" ZN B 501 " Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 648 Unresolved non-hydrogen angles: 824 Unresolved non-hydrogen dihedrals: 524 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 355 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9622 SG CYS B 323 50.818 30.708 18.486 1.00157.30 S ATOM 9638 SG CYS B 326 48.791 27.319 18.587 1.00163.96 S ATOM 9904 SG CYS B 391 52.433 27.620 17.040 1.00184.67 S ATOM 9920 SG CYS B 394 49.311 28.958 15.432 1.00187.88 S Time building chain proxies: 5.94, per 1000 atoms: 0.59 Number of scatterers: 10112 At special positions: 0 Unit cell: (96.6, 106.95, 151.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 48 16.00 O 1943 8.00 N 1780 7.00 C 6340 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 - 3.50 Amino acid : False - 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: 4.10 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 391 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 326 " Number of angles added : 6 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 29 sheets defined 11.3% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1059 Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1101 through 1109 Processing helix chain 'A' and resid 1123 through 1126 removed outlier: 4.281A pdb=" N ALA A1126 " --> pdb=" O GLU A1123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1123 through 1126' Processing helix chain 'A' and resid 1127 through 1138 Processing helix chain 'B' and resid 103 through 117 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.508A pdb=" N PHE B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.509A pdb=" N ASN B 236 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.677A pdb=" N TYR B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 263 removed outlier: 3.562A pdb=" N GLU B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 303 through 316 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009 removed outlier: 6.999A pdb=" N GLY A1031 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE A1007 " --> pdb=" O LEU A1029 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU A1029 " --> pdb=" O PHE A1007 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A1030 " --> pdb=" O GLY A1038 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.528A pdb=" N ILE A 41 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 53 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 65 removed outlier: 6.501A pdb=" N LEU A 80 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET A 64 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N PHE A 78 " --> pdb=" O MET A 64 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.600A pdb=" N ILE A 121 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169 removed outlier: 7.026A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 194 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 164 through 169 removed outlier: 7.026A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.572A pdb=" N MET A 218 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 258 through 263 removed outlier: 3.529A pdb=" N CYS A 260 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 306 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET A 282 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU A 304 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 284 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL A 302 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 321 through 324 removed outlier: 6.538A pdb=" N SER A 331 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR A 352 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 364 through 365 removed outlier: 3.690A pdb=" N ARG A 391 " --> pdb=" O HIS A 711 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS A 711 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 396 through 403 removed outlier: 6.820A pdb=" N ILE A 701 " --> pdb=" O HIS A 399 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER A 401 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU A 699 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AB4, first strand: chain 'A' and resid 467 through 471 removed outlier: 4.383A pdb=" N VAL A 476 " --> pdb=" O TRP A 490 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP A 490 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 488 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER A 480 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU A 486 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 498 through 503 removed outlier: 4.157A pdb=" N VAL A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU A 516 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N HIS A 531 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N TYR A 518 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 529 " --> pdb=" O TYR A 518 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 556 through 560 removed outlier: 3.601A pdb=" N SER A 565 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 566 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS A 579 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 568 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 588 through 594 removed outlier: 3.531A pdb=" N SER A 590 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL A 629 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 637 through 639 removed outlier: 3.615A pdb=" N SER A 669 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 724 through 727 Processing sheet with id=AC1, first strand: chain 'A' and resid 724 through 727 removed outlier: 3.773A pdb=" N ILE A 794 " --> pdb=" O PHE A 733 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 737 " --> pdb=" O ASN A 790 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 790 " --> pdb=" O SER A 737 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N HIS A 789 " --> pdb=" O GLN A 806 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLN A 806 " --> pdb=" O HIS A 789 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU A 791 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 804 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A 793 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 811 through 813 Processing sheet with id=AC3, first strand: chain 'A' and resid 811 through 813 removed outlier: 3.638A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY A 846 " --> pdb=" O GLU A 865 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU A 865 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 848 " --> pdb=" O GLU A 863 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU A 863 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 850 " --> pdb=" O VAL A 861 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 870 through 876 removed outlier: 4.387A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 913 through 917 removed outlier: 3.569A pdb=" N LYS A 917 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 945 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 936 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN A 941 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 957 through 959 removed outlier: 6.499A pdb=" N LEU A 974 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 997 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 976 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AC8, first strand: chain 'B' and resid 65 through 66 removed outlier: 14.037A pdb=" N THR B 119 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL B 80 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ALA B 121 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 123 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 180 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN B 178 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 169 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN B 183 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL B 167 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 155 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 101 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 157 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 65 through 66 removed outlier: 7.134A pdb=" N GLY B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ARG B 164 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR B 138 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS B 158 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR B 144 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS B 156 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU B 146 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 154 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLN B 148 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 155 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 101 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 157 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 320 through 322 removed outlier: 4.150A pdb=" N THR B 332 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 368 through 371 removed outlier: 3.671A pdb=" N GLY B 399 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N CYS B 391 " --> pdb=" O HIS B 397 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS B 397 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP B 400 " --> pdb=" O GLY B 416 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.36 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3513 1.34 - 1.46: 2190 1.46 - 1.58: 4511 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 10284 Sorted by residual: bond pdb=" CG1 ILE B 257 " pdb=" CD1 ILE B 257 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.53e+00 bond pdb=" CG ARG A 198 " pdb=" CD ARG A 198 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.40e-01 bond pdb=" CB ASP A 243 " pdb=" CG ASP A 243 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.66e-01 bond pdb=" CB ASP A 986 " pdb=" CG ASP A 986 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.88e-01 bond pdb=" CB ARG A 198 " pdb=" CG ARG A 198 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.82e-01 ... (remaining 10279 not shown) Histogram of bond angle deviations from ideal: 99.44 - 108.04: 419 108.04 - 116.64: 6997 116.64 - 125.24: 6512 125.24 - 133.84: 124 133.84 - 142.44: 14 Bond angle restraints: 14066 Sorted by residual: angle pdb=" C LEU B 423 " pdb=" N PRO B 424 " pdb=" CA PRO B 424 " ideal model delta sigma weight residual 127.00 142.44 -15.44 2.40e+00 1.74e-01 4.14e+01 angle pdb=" N ILE B 398 " pdb=" CA ILE B 398 " pdb=" C ILE B 398 " ideal model delta sigma weight residual 113.47 109.30 4.17 1.01e+00 9.80e-01 1.71e+01 angle pdb=" C GLY A1119 " pdb=" N MET A1120 " pdb=" CA MET A1120 " ideal model delta sigma weight residual 121.54 128.41 -6.87 1.91e+00 2.74e-01 1.29e+01 angle pdb=" N ASP A1127 " pdb=" CA ASP A1127 " pdb=" C ASP A1127 " ideal model delta sigma weight residual 114.56 110.40 4.16 1.27e+00 6.20e-01 1.07e+01 angle pdb=" N GLU A1107 " pdb=" CA GLU A1107 " pdb=" CB GLU A1107 " ideal model delta sigma weight residual 110.28 114.87 -4.59 1.55e+00 4.16e-01 8.77e+00 ... (remaining 14061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5706 17.89 - 35.78: 354 35.78 - 53.67: 61 53.67 - 71.56: 13 71.56 - 89.45: 10 Dihedral angle restraints: 6144 sinusoidal: 1847 harmonic: 4297 Sorted by residual: dihedral pdb=" CA TYR A 828 " pdb=" C TYR A 828 " pdb=" N PHE A 829 " pdb=" CA PHE A 829 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA LEU A1112 " pdb=" C LEU A1112 " pdb=" N GLN A1113 " pdb=" CA GLN A1113 " ideal model delta harmonic sigma weight residual 180.00 -160.28 -19.72 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA VAL A 836 " pdb=" C VAL A 836 " pdb=" N TYR A 837 " pdb=" CA TYR A 837 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 6141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1293 0.048 - 0.096: 267 0.096 - 0.144: 108 0.144 - 0.192: 1 0.192 - 0.240: 1 Chirality restraints: 1670 Sorted by residual: chirality pdb=" CB ILE A 220 " pdb=" CA ILE A 220 " pdb=" CG1 ILE A 220 " pdb=" CG2 ILE A 220 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL A 957 " pdb=" CA VAL A 957 " pdb=" CG1 VAL A 957 " pdb=" CG2 VAL A 957 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE A 848 " pdb=" N ILE A 848 " pdb=" C ILE A 848 " pdb=" CB ILE A 848 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1667 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 416 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO A 417 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 417 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 417 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 522 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO A 523 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 276 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO B 277 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 277 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 277 " 0.024 5.00e-02 4.00e+02 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1466 2.77 - 3.30: 9372 3.30 - 3.83: 15159 3.83 - 4.37: 16829 4.37 - 4.90: 31226 Nonbonded interactions: 74052 Sorted by model distance: nonbonded pdb=" OH TYR B 227 " pdb=" OD2 ASP B 249 " model vdw 2.231 2.440 nonbonded pdb=" OE2 GLU A 277 " pdb=" NH1 ARG A 279 " model vdw 2.270 2.520 nonbonded pdb=" OD1 ASP A 986 " pdb=" N GLU A 987 " model vdw 2.290 2.520 nonbonded pdb=" NH1 ARG A 301 " pdb=" OE2 GLU A 303 " model vdw 2.309 2.520 nonbonded pdb=" NZ LYS A 141 " pdb=" OD1 ASN A 156 " model vdw 2.320 2.520 ... (remaining 74047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.950 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 35.130 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 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 : 0.003 0.048 10284 Z= 0.179 Angle : 0.578 15.443 14066 Z= 0.310 Chirality : 0.045 0.240 1670 Planarity : 0.004 0.046 1880 Dihedral : 13.055 89.454 3360 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.83 % Rotamer: Outliers : 0.12 % Allowed : 0.36 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.23), residues: 1476 helix: 1.38 (0.45), residues: 151 sheet: -1.39 (0.23), residues: 539 loop : -1.37 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 207 HIS 0.002 0.001 HIS A 805 PHE 0.016 0.002 PHE B 208 TYR 0.025 0.001 TYR A 837 ARG 0.013 0.001 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.297 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.2707 time to fit residues: 60.6405 Evaluate side-chains 123 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 40.0000 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 30.0000 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.0010 chunk 44 optimal weight: 50.0000 chunk 70 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 0.0670 overall best weight: 0.9928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 GLN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10284 Z= 0.228 Angle : 0.572 7.650 14066 Z= 0.300 Chirality : 0.046 0.228 1670 Planarity : 0.004 0.050 1880 Dihedral : 4.022 20.097 1554 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 1.68 % Allowed : 8.27 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.22), residues: 1476 helix: 1.06 (0.43), residues: 158 sheet: -1.25 (0.23), residues: 536 loop : -1.53 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 386 HIS 0.003 0.001 HIS A1070 PHE 0.014 0.002 PHE A 799 TYR 0.014 0.001 TYR A 837 ARG 0.009 0.000 ARG A 947 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.144 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 135 average time/residue: 0.2698 time to fit residues: 50.1751 Evaluate side-chains 128 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0950 time to fit residues: 3.6606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.0770 chunk 41 optimal weight: 9.9990 chunk 111 optimal weight: 30.0000 chunk 91 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 145 optimal weight: 20.0000 chunk 119 optimal weight: 40.0000 chunk 133 optimal weight: 10.0000 chunk 45 optimal weight: 40.0000 chunk 108 optimal weight: 2.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 GLN A1034 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10284 Z= 0.234 Angle : 0.552 7.925 14066 Z= 0.288 Chirality : 0.046 0.185 1670 Planarity : 0.004 0.051 1880 Dihedral : 3.993 20.058 1554 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.83 % Rotamer: Outliers : 0.60 % Allowed : 11.51 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.22), residues: 1476 helix: 1.02 (0.43), residues: 158 sheet: -1.20 (0.23), residues: 530 loop : -1.55 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 386 HIS 0.003 0.001 HIS A1009 PHE 0.012 0.002 PHE A 829 TYR 0.014 0.001 TYR A 346 ARG 0.004 0.000 ARG A 947 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 1.225 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 126 average time/residue: 0.2568 time to fit residues: 45.2365 Evaluate side-chains 116 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0938 time to fit residues: 1.9725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN A 743 GLN ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 GLN B 198 GLN B 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10284 Z= 0.403 Angle : 0.637 8.120 14066 Z= 0.328 Chirality : 0.048 0.193 1670 Planarity : 0.004 0.050 1880 Dihedral : 4.378 20.926 1554 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.59 % Favored : 92.34 % Rotamer: Outliers : 1.80 % Allowed : 13.79 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.22), residues: 1476 helix: 0.82 (0.43), residues: 158 sheet: -1.36 (0.22), residues: 541 loop : -1.63 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 386 HIS 0.004 0.001 HIS A 789 PHE 0.018 0.002 PHE A 169 TYR 0.022 0.002 TYR A 346 ARG 0.006 0.000 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.249 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 125 average time/residue: 0.2698 time to fit residues: 46.5440 Evaluate side-chains 127 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1015 time to fit residues: 3.9413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 30.0000 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 128 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 GLN ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10284 Z= 0.230 Angle : 0.550 7.698 14066 Z= 0.287 Chirality : 0.045 0.162 1670 Planarity : 0.004 0.049 1880 Dihedral : 4.120 20.983 1554 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.57 % Favored : 93.36 % Rotamer: Outliers : 0.96 % Allowed : 14.39 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.22), residues: 1476 helix: 0.92 (0.43), residues: 157 sheet: -1.30 (0.22), residues: 538 loop : -1.62 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 207 HIS 0.003 0.001 HIS A1009 PHE 0.014 0.002 PHE A 771 TYR 0.013 0.001 TYR A 346 ARG 0.008 0.000 ARG A 947 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 131 average time/residue: 0.2612 time to fit residues: 47.3112 Evaluate side-chains 124 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1021 time to fit residues: 2.7382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.3682 > 50: distance: 25 - 80: 27.573 distance: 32 - 35: 17.963 distance: 35 - 36: 9.160 distance: 36 - 37: 34.289 distance: 36 - 39: 33.033 distance: 37 - 38: 56.796 distance: 37 - 40: 10.043 distance: 40 - 41: 6.147 distance: 41 - 42: 40.563 distance: 41 - 44: 7.099 distance: 42 - 43: 34.302 distance: 42 - 45: 12.396 distance: 45 - 46: 14.535 distance: 46 - 47: 34.550 distance: 46 - 49: 23.997 distance: 47 - 48: 20.111 distance: 47 - 50: 41.341 distance: 50 - 51: 10.127 distance: 50 - 56: 13.944 distance: 51 - 52: 43.298 distance: 51 - 54: 16.820 distance: 52 - 53: 18.241 distance: 52 - 57: 25.442 distance: 54 - 55: 43.319 distance: 55 - 56: 53.121 distance: 57 - 58: 41.046 distance: 58 - 59: 18.085 distance: 58 - 61: 35.577 distance: 59 - 60: 30.453 distance: 59 - 62: 51.834 distance: 62 - 63: 20.807 distance: 63 - 64: 24.626 distance: 63 - 66: 31.293 distance: 64 - 65: 20.891 distance: 64 - 67: 33.280 distance: 67 - 68: 18.233 distance: 68 - 69: 23.595 distance: 68 - 71: 13.595 distance: 69 - 70: 31.429 distance: 69 - 72: 12.143 distance: 72 - 73: 31.126 distance: 73 - 74: 34.158 distance: 73 - 76: 21.950 distance: 74 - 75: 34.751 distance: 74 - 77: 18.899 distance: 77 - 78: 33.210 distance: 78 - 79: 43.967 distance: 78 - 81: 34.426 distance: 79 - 80: 12.659 distance: 79 - 82: 7.542 distance: 82 - 83: 23.956 distance: 83 - 84: 20.650 distance: 83 - 86: 16.051 distance: 84 - 85: 14.900 distance: 84 - 87: 13.552