Starting phenix.real_space_refine on Tue May 20 20:09:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x6a_22074/05_2025/6x6a_22074.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x6a_22074/05_2025/6x6a_22074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x6a_22074/05_2025/6x6a_22074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x6a_22074/05_2025/6x6a_22074.map" model { file = "/net/cci-nas-00/data/ceres_data/6x6a_22074/05_2025/6x6a_22074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x6a_22074/05_2025/6x6a_22074.cif" } resolution = 3.6 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= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 13051 2.51 5 N 3429 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20240 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6816 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 791} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1068 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 10, 'TRANS': 123} Chain: "G" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1107 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1136 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 132} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 6816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6816 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 791} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1053 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 123} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 127} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1141 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 132} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.49, per 1000 atoms: 0.62 Number of scatterers: 20240 At special positions: 0 Unit cell: (129.525, 161.7, 114.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3660 8.00 N 3429 7.00 C 13051 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: 4.66 Conformation dependent library (CDL) restraints added in 2.7 seconds 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4696 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 39 sheets defined 18.7% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 30 through 49 removed outlier: 4.191A pdb=" N TYR A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU A 47 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.540A pdb=" N VAL A 120 " --> pdb=" O HIS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 661 through 671 removed outlier: 3.608A pdb=" N ASN A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 700 through 716 Processing helix chain 'A' and resid 730 through 743 Processing helix chain 'A' and resid 758 through 762 Processing helix chain 'A' and resid 763 through 771 removed outlier: 4.295A pdb=" N ARG A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 785 Processing helix chain 'A' and resid 786 through 793 removed outlier: 3.825A pdb=" N VAL A 790 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLU A 791 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 827 removed outlier: 4.297A pdb=" N THR A 816 " --> pdb=" O HIS A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 863 Processing helix chain 'B' and resid 1132 through 1137 removed outlier: 3.565A pdb=" N GLY B1137 " --> pdb=" O ASP B1133 " (cutoff:3.500A) Processing helix chain 'G' and resid 1256 through 1270 Processing helix chain 'C' and resid 1258 through 1270 removed outlier: 4.133A pdb=" N ALA C1262 " --> pdb=" O SER C1258 " (cutoff:3.500A) Processing helix chain 'C' and resid 1295 through 1300 removed outlier: 4.120A pdb=" N MET C1299 " --> pdb=" O SER C1295 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 49 removed outlier: 3.801A pdb=" N TYR D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.544A pdb=" N VAL D 120 " --> pdb=" O HIS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 661 through 671 removed outlier: 3.622A pdb=" N ASN D 665 " --> pdb=" O TYR D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 691 Processing helix chain 'D' and resid 692 through 694 No H-bonds generated for 'chain 'D' and resid 692 through 694' Processing helix chain 'D' and resid 700 through 716 Processing helix chain 'D' and resid 730 through 743 Processing helix chain 'D' and resid 758 through 762 Processing helix chain 'D' and resid 763 through 771 removed outlier: 4.095A pdb=" N ARG D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 785 Processing helix chain 'D' and resid 786 through 793 removed outlier: 4.033A pdb=" N VAL D 790 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLU D 791 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 827 removed outlier: 4.393A pdb=" N THR D 816 " --> pdb=" O HIS D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 863 Processing helix chain 'E' and resid 1132 through 1137 Processing helix chain 'E' and resid 1141 through 1145 Processing helix chain 'I' and resid 1256 through 1270 Processing helix chain 'F' and resid 1228 through 1236 removed outlier: 3.788A pdb=" N SER F1233 " --> pdb=" O ILE F1229 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL F1234 " --> pdb=" O PRO F1230 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F1236 " --> pdb=" O THR F1232 " (cutoff:3.500A) Processing helix chain 'F' and resid 1258 through 1270 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 60 removed outlier: 5.954A pdb=" N ASP A 55 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 75 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.652A pdb=" N LEU A 100 " --> pdb=" O LEU B1194 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL G1217 " --> pdb=" O ALA B1185 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE B1187 " --> pdb=" O LEU G1215 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU G1215 " --> pdb=" O PHE B1187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 4.135A pdb=" N ALA A 155 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 193 removed outlier: 6.491A pdb=" N SER A 202 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE A 193 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE A 200 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.679A pdb=" N SER A 263 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 258 removed outlier: 9.093A pdb=" N LEU A 317 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 338 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 287 through 291 Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 357 removed outlier: 5.470A pdb=" N ILE A 352 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 369 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 354 " --> pdb=" O MET A 367 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 376 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU A 414 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU A 378 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 427 through 429 removed outlier: 3.527A pdb=" N HIS A 453 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 507 Processing sheet with id=AB2, first strand: chain 'A' and resid 547 through 552 removed outlier: 6.458A pdb=" N VAL A 572 " --> pdb=" O MET A 595 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS A 576 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE A 591 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 578 " --> pdb=" O PRO A 589 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 609 through 614 removed outlier: 4.457A pdb=" N ILE A 677 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N HIS A 637 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG A 723 " --> pdb=" O HIS A 637 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TRP A 729 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA A 750 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU A 803 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA A 752 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY A 805 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1089 through 1092 removed outlier: 3.671A pdb=" N VAL B1091 " --> pdb=" O LEU B1097 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU B1097 " --> pdb=" O VAL B1091 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B1123 " --> pdb=" O PHE B1102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1116 through 1118 removed outlier: 3.837A pdb=" N VAL B1164 " --> pdb=" O LEU B1207 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B1199 " --> pdb=" O VAL B1206 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 1230 through 1231 removed outlier: 3.550A pdb=" N LEU G1284 " --> pdb=" O VAL G1231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 1238 through 1239 removed outlier: 3.531A pdb=" N VAL G1273 " --> pdb=" O HIS G1239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 1247 through 1251 removed outlier: 3.512A pdb=" N TYR G1324 " --> pdb=" O GLU G1301 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU G1301 " --> pdb=" O TYR G1324 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 1306 through 1308 removed outlier: 4.176A pdb=" N VAL G1336 " --> pdb=" O TRP G1346 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP G1346 " --> pdb=" O VAL G1336 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP G1338 " --> pdb=" O LEU G1344 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU G1344 " --> pdb=" O ASP G1338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 1238 through 1241 removed outlier: 6.069A pdb=" N VAL C1246 " --> pdb=" O VAL C1325 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1306 through 1309 removed outlier: 3.851A pdb=" N LEU C1309 " --> pdb=" O CYS C1288 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS C1288 " --> pdb=" O LEU C1309 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE C1332 " --> pdb=" O VAL C1350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 54 through 60 removed outlier: 4.291A pdb=" N PHE D 56 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR D 73 " --> pdb=" O PHE D 56 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE D 58 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG D 71 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLN D 60 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N SER D 69 " --> pdb=" O GLN D 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 100 through 103 removed outlier: 3.686A pdb=" N LEU D 100 " --> pdb=" O LEU E1194 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 Processing sheet with id=AC6, first strand: chain 'D' and resid 189 through 193 removed outlier: 6.463A pdb=" N SER D 202 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE D 193 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE D 200 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 237 through 239 Processing sheet with id=AC8, first strand: chain 'D' and resid 256 through 258 removed outlier: 9.030A pdb=" N LEU D 317 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU D 338 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 287 through 291 Processing sheet with id=AD1, first strand: chain 'D' and resid 351 through 357 removed outlier: 6.686A pdb=" N MET D 367 " --> pdb=" O ALA D 353 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA D 355 " --> pdb=" O TRP D 365 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP D 365 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU D 376 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU D 414 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 378 " --> pdb=" O VAL D 412 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 427 through 429 Processing sheet with id=AD3, first strand: chain 'D' and resid 505 through 507 Processing sheet with id=AD4, first strand: chain 'D' and resid 547 through 552 removed outlier: 6.586A pdb=" N VAL D 572 " --> pdb=" O MET D 595 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS D 576 " --> pdb=" O PHE D 591 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE D 591 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER D 578 " --> pdb=" O PRO D 589 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 609 through 614 removed outlier: 4.309A pdb=" N TYR D 622 " --> pdb=" O ASP D 678 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE D 677 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N HIS D 637 " --> pdb=" O LEU D 721 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG D 723 " --> pdb=" O HIS D 637 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL D 749 " --> pdb=" O SER D 722 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 724 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE D 751 " --> pdb=" O VAL D 724 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE D 726 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY D 753 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY D 728 " --> pdb=" O GLY D 753 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA D 750 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU D 803 " --> pdb=" O ALA D 750 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA D 752 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N GLY D 805 " --> pdb=" O ALA D 752 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 1116 through 1118 removed outlier: 3.646A pdb=" N CYS E1116 " --> pdb=" O HIS E1165 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 1199 through 1200 removed outlier: 3.934A pdb=" N ARG E1199 " --> pdb=" O VAL E1206 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 1230 through 1231 removed outlier: 3.773A pdb=" N LEU I1284 " --> pdb=" O VAL I1231 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1237 through 1238 Processing sheet with id=AE1, first strand: chain 'I' and resid 1290 through 1294 removed outlier: 7.476A pdb=" N VAL I1336 " --> pdb=" O VAL I1345 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 1273 through 1274 removed outlier: 3.997A pdb=" N THR F1247 " --> pdb=" O ARG F1240 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL F1246 " --> pdb=" O VAL F1325 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 1290 through 1293 removed outlier: 6.616A pdb=" N ASP F1338 " --> pdb=" O LEU F1344 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU F1344 " --> pdb=" O ASP F1338 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1779 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: 8.39 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3347 1.32 - 1.44: 5827 1.44 - 1.57: 11501 1.57 - 1.69: 7 1.69 - 1.81: 156 Bond restraints: 20838 Sorted by residual: bond pdb=" C TYR A 731 " pdb=" O TYR A 731 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.17e-02 7.31e+03 1.48e+01 bond pdb=" C GLY A 728 " pdb=" O GLY A 728 " ideal model delta sigma weight residual 1.233 1.196 0.037 9.80e-03 1.04e+04 1.40e+01 bond pdb=" C ARG A 371 " pdb=" O ARG A 371 " ideal model delta sigma weight residual 1.244 1.211 0.033 9.80e-03 1.04e+04 1.11e+01 bond pdb=" N ASN E1140 " pdb=" CA ASN E1140 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.60e+00 bond pdb=" C SER A 730 " pdb=" O SER A 730 " ideal model delta sigma weight residual 1.235 1.197 0.039 1.26e-02 6.30e+03 9.48e+00 ... (remaining 20833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 26818 2.68 - 5.35: 1254 5.35 - 8.03: 180 8.03 - 10.71: 41 10.71 - 13.38: 5 Bond angle restraints: 28298 Sorted by residual: angle pdb=" N ASN E1140 " pdb=" CA ASN E1140 " pdb=" C ASN E1140 " ideal model delta sigma weight residual 112.75 124.46 -11.71 1.36e+00 5.41e-01 7.42e+01 angle pdb=" N LYS I1220 " pdb=" CA LYS I1220 " pdb=" C LYS I1220 " ideal model delta sigma weight residual 111.28 120.22 -8.94 1.09e+00 8.42e-01 6.73e+01 angle pdb=" N TRP D 729 " pdb=" CA TRP D 729 " pdb=" C TRP D 729 " ideal model delta sigma weight residual 111.96 123.41 -11.45 1.41e+00 5.03e-01 6.59e+01 angle pdb=" CA TRP D 729 " pdb=" C TRP D 729 " pdb=" N SER D 730 " ideal model delta sigma weight residual 117.34 126.21 -8.87 1.22e+00 6.72e-01 5.28e+01 angle pdb=" N ILE I1302 " pdb=" CA ILE I1302 " pdb=" C ILE I1302 " ideal model delta sigma weight residual 107.75 117.75 -10.00 1.42e+00 4.96e-01 4.96e+01 ... (remaining 28293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11053 17.76 - 35.52: 1061 35.52 - 53.28: 169 53.28 - 71.03: 47 71.03 - 88.79: 12 Dihedral angle restraints: 12342 sinusoidal: 5024 harmonic: 7318 Sorted by residual: dihedral pdb=" CA TYR D 770 " pdb=" C TYR D 770 " pdb=" N MET D 771 " pdb=" CA MET D 771 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LEU C1300 " pdb=" C LEU C1300 " pdb=" N GLU C1301 " pdb=" CA GLU C1301 " ideal model delta harmonic sigma weight residual -180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA SER I1233 " pdb=" C SER I1233 " pdb=" N VAL I1234 " pdb=" CA VAL I1234 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 12339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2410 0.093 - 0.185: 506 0.185 - 0.278: 77 0.278 - 0.370: 16 0.370 - 0.463: 4 Chirality restraints: 3013 Sorted by residual: chirality pdb=" CB ILE C1302 " pdb=" CA ILE C1302 " pdb=" CG1 ILE C1302 " pdb=" CG2 ILE C1302 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CA ASN E1140 " pdb=" N ASN E1140 " pdb=" C ASN E1140 " pdb=" CB ASN E1140 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB ILE D 426 " pdb=" CA ILE D 426 " pdb=" CG1 ILE D 426 " pdb=" CG2 ILE D 426 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 3010 not shown) Planarity restraints: 3657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL I1292 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.64e+01 pdb=" C VAL I1292 " -0.070 2.00e-02 2.50e+03 pdb=" O VAL I1292 " 0.026 2.00e-02 2.50e+03 pdb=" N SER I1293 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 393 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C GLU A 393 " -0.065 2.00e-02 2.50e+03 pdb=" O GLU A 393 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A 394 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 393 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C GLU D 393 " 0.062 2.00e-02 2.50e+03 pdb=" O GLU D 393 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU D 394 " -0.021 2.00e-02 2.50e+03 ... (remaining 3654 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2520 2.74 - 3.28: 19071 3.28 - 3.82: 35094 3.82 - 4.36: 41632 4.36 - 4.90: 71084 Nonbonded interactions: 169401 Sorted by model distance: nonbonded pdb=" OH TYR A 644 " pdb=" O SER C1213 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR D 73 " pdb=" OD2 ASP D 164 " model vdw 2.210 3.040 nonbonded pdb=" CG TYR G1238 " pdb=" OE2 GLU G1267 " model vdw 2.213 3.260 nonbonded pdb=" O LYS A 348 " pdb=" OD1 ASP A 370 " model vdw 2.225 3.040 nonbonded pdb=" OG SER D 230 " pdb=" OD1 ASN D 231 " model vdw 2.254 3.040 ... (remaining 169396 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and ((resid 1079 through 1080 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1081 through 1212)) selection = chain 'E' } ncs_group { reference = (chain 'C' and ((resid 1213 and (name CA or name C or name O or name CB or name \ OG )) or resid 1214 through 1276 or (resid 1277 and (name N or name CA or name C \ or name O or name CB )) or resid 1278 through 1350)) selection = (chain 'F' and ((resid 1213 and (name CA or name C or name O or name CB or name \ OG )) or resid 1214 through 1225 or (resid 1226 and (name N or name CA or name C \ or name O or name CB )) or resid 1227 or (resid 1228 through 1229 and (name N o \ r name CA or name C or name O or name CB )) or resid 1230 through 1350)) selection = (chain 'G' and (resid 1213 through 1219 or (resid 1220 and (name N or name CA or \ name C or name O or name CB )) or resid 1221 through 1225 or (resid 1226 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1227 or (resid 1228 \ through 1229 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 230 through 1276 or (resid 1277 and (name N or name CA or name C or name O or na \ me CB )) or resid 1278 through 1350)) selection = (chain 'I' and (resid 1213 through 1219 or (resid 1220 and (name N or name CA or \ name C or name O or name CB )) or resid 1221 through 1225 or (resid 1226 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1227 or (resid 1228 \ through 1229 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 230 through 1350)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 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: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 47.340 Find NCS groups from input model: 0.930 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.010 0.112 20838 Z= 0.444 Angle : 1.291 13.382 28298 Z= 0.727 Chirality : 0.078 0.463 3013 Planarity : 0.009 0.085 3657 Dihedral : 14.434 88.793 7646 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.50 % Favored : 92.38 % Rotamer: Outliers : 0.45 % Allowed : 1.27 % Favored : 98.28 % 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: -2.80 (0.15), residues: 2508 helix: -1.59 (0.23), residues: 378 sheet: -2.25 (0.17), residues: 724 loop : -1.66 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP A 375 HIS 0.024 0.003 HIS A 111 PHE 0.056 0.004 PHE D 711 TYR 0.056 0.004 TYR A 781 ARG 0.020 0.001 ARG G1333 Details of bonding type rmsd hydrogen bonds : bond 0.14437 ( 668) hydrogen bonds : angle 8.57491 ( 1779) covalent geometry : bond 0.01009 (20838) covalent geometry : angle 1.29059 (28298) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 267 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8060 (t0) cc_final: 0.7526 (t70) REVERT: A 738 MET cc_start: 0.8501 (mmm) cc_final: 0.8223 (mmm) REVERT: B 1099 ARG cc_start: 0.7178 (mtp-110) cc_final: 0.6868 (mtp180) REVERT: B 1119 MET cc_start: 0.6018 (ptp) cc_final: 0.5776 (pmm) REVERT: B 1178 ASP cc_start: 0.7384 (t0) cc_final: 0.7111 (t70) REVERT: B 1203 HIS cc_start: 0.6519 (m-70) cc_final: 0.6314 (m170) REVERT: G 1263 ILE cc_start: 0.7810 (pt) cc_final: 0.7471 (pt) REVERT: G 1330 SER cc_start: 0.7451 (t) cc_final: 0.7018 (m) REVERT: C 1260 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7124 (ttt-90) REVERT: C 1286 MET cc_start: 0.3543 (ptt) cc_final: 0.3216 (ptm) REVERT: D 251 ASP cc_start: 0.8025 (m-30) cc_final: 0.7723 (t0) REVERT: D 684 GLN cc_start: 0.7870 (mp10) cc_final: 0.7034 (mp10) REVERT: E 1096 ASN cc_start: 0.7374 (t0) cc_final: 0.7122 (t0) REVERT: E 1119 MET cc_start: 0.5535 (tpp) cc_final: 0.5066 (mpp) REVERT: I 1227 ARG cc_start: 0.6008 (tpp-160) cc_final: 0.5740 (tpp-160) REVERT: I 1338 ASP cc_start: 0.6554 (t0) cc_final: 0.6299 (t0) REVERT: F 1289 ARG cc_start: 0.7427 (mtt180) cc_final: 0.7157 (mtm-85) outliers start: 10 outliers final: 5 residues processed: 276 average time/residue: 0.3660 time to fit residues: 150.3361 Evaluate side-chains 208 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 203 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 1217 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain I residue 1320 PHE Chi-restraints excluded: chain I residue 1332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 225 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 516 GLN A 810 ASN ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1140 ASN B1204 HIS ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN E1140 ASN E1165 HIS I1335 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.116990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082902 restraints weight = 47828.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.081048 restraints weight = 26324.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.082808 restraints weight = 20867.030| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20838 Z= 0.160 Angle : 0.685 10.270 28298 Z= 0.358 Chirality : 0.047 0.185 3013 Planarity : 0.006 0.069 3657 Dihedral : 6.356 38.895 2751 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.91 % Allowed : 8.20 % Favored : 90.89 % 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: -2.01 (0.16), residues: 2508 helix: -0.29 (0.26), residues: 382 sheet: -1.80 (0.17), residues: 764 loop : -1.29 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 375 HIS 0.006 0.001 HIS D 54 PHE 0.018 0.002 PHE I1228 TYR 0.017 0.002 TYR C1290 ARG 0.007 0.001 ARG A 769 Details of bonding type rmsd hydrogen bonds : bond 0.04554 ( 668) hydrogen bonds : angle 6.87397 ( 1779) covalent geometry : bond 0.00361 (20838) covalent geometry : angle 0.68490 (28298) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8167 (t0) cc_final: 0.7651 (t70) REVERT: A 738 MET cc_start: 0.8908 (mmm) cc_final: 0.8657 (mmm) REVERT: B 1119 MET cc_start: 0.6353 (ptp) cc_final: 0.6053 (pmm) REVERT: B 1187 PHE cc_start: 0.7925 (m-80) cc_final: 0.7669 (m-10) REVERT: B 1194 LEU cc_start: 0.8250 (mt) cc_final: 0.7835 (mt) REVERT: G 1251 TYR cc_start: 0.7181 (m-80) cc_final: 0.6471 (m-80) REVERT: C 1260 ARG cc_start: 0.7683 (mtp180) cc_final: 0.7333 (ttt-90) REVERT: C 1264 ASP cc_start: 0.6462 (m-30) cc_final: 0.6202 (m-30) REVERT: C 1286 MET cc_start: 0.3587 (ptt) cc_final: 0.3187 (ptm) REVERT: C 1323 PHE cc_start: 0.5024 (t80) cc_final: 0.4698 (t80) REVERT: D 251 ASP cc_start: 0.8079 (m-30) cc_final: 0.7704 (t0) REVERT: D 684 GLN cc_start: 0.7751 (mp10) cc_final: 0.7223 (mp10) REVERT: D 738 MET cc_start: 0.9302 (mmm) cc_final: 0.9087 (mmm) REVERT: E 1096 ASN cc_start: 0.7483 (t0) cc_final: 0.6967 (t0) REVERT: E 1119 MET cc_start: 0.5428 (tpp) cc_final: 0.4804 (mtm) REVERT: E 1184 MET cc_start: 0.7678 (tmm) cc_final: 0.7467 (tmm) REVERT: I 1322 GLU cc_start: 0.7572 (pp20) cc_final: 0.7364 (pp20) REVERT: I 1338 ASP cc_start: 0.6352 (t0) cc_final: 0.6105 (t0) REVERT: F 1289 ARG cc_start: 0.7371 (mtt180) cc_final: 0.7075 (mtm-85) REVERT: F 1333 ARG cc_start: 0.7440 (ttm170) cc_final: 0.7181 (ttt180) REVERT: F 1335 GLN cc_start: 0.6966 (mp10) cc_final: 0.6248 (mp10) outliers start: 20 outliers final: 13 residues processed: 240 average time/residue: 0.3804 time to fit residues: 137.5100 Evaluate side-chains 223 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain G residue 1259 ILE Chi-restraints excluded: chain G residue 1299 MET Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 433 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain I residue 1320 PHE Chi-restraints excluded: chain I residue 1332 ILE Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1239 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 187 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 222 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 243 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 237 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 810 ASN ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 HIS ** B1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN D 374 GLN D 516 GLN D 798 ASN E1183 GLN ** I1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.115695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.081384 restraints weight = 47950.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.079700 restraints weight = 26313.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.080924 restraints weight = 21387.220| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20838 Z= 0.192 Angle : 0.654 9.997 28298 Z= 0.338 Chirality : 0.046 0.205 3013 Planarity : 0.006 0.082 3657 Dihedral : 5.931 37.042 2746 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.22 % Allowed : 12.69 % Favored : 86.08 % 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: -1.69 (0.16), residues: 2508 helix: 0.21 (0.27), residues: 372 sheet: -1.59 (0.18), residues: 759 loop : -1.15 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 375 HIS 0.008 0.001 HIS D 54 PHE 0.023 0.002 PHE G1272 TYR 0.016 0.002 TYR D 835 ARG 0.014 0.001 ARG I1333 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 668) hydrogen bonds : angle 6.39866 ( 1779) covalent geometry : bond 0.00443 (20838) covalent geometry : angle 0.65355 (28298) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8158 (t0) cc_final: 0.7601 (t70) REVERT: A 738 MET cc_start: 0.8988 (mmm) cc_final: 0.8777 (mmm) REVERT: B 1187 PHE cc_start: 0.7861 (m-80) cc_final: 0.7644 (m-10) REVERT: G 1251 TYR cc_start: 0.7165 (m-80) cc_final: 0.6649 (m-80) REVERT: C 1260 ARG cc_start: 0.7648 (mtp180) cc_final: 0.7342 (ttt-90) REVERT: C 1268 MET cc_start: 0.4138 (mmp) cc_final: 0.3876 (mmt) REVERT: C 1272 PHE cc_start: 0.4720 (m-80) cc_final: 0.4308 (m-80) REVERT: D 251 ASP cc_start: 0.8099 (m-30) cc_final: 0.7741 (t0) REVERT: D 771 MET cc_start: 0.7662 (mtt) cc_final: 0.7446 (mtt) REVERT: E 1096 ASN cc_start: 0.7370 (t0) cc_final: 0.6873 (t0) REVERT: I 1321 SER cc_start: 0.6937 (m) cc_final: 0.6448 (t) REVERT: I 1336 VAL cc_start: 0.8875 (m) cc_final: 0.8504 (m) REVERT: I 1338 ASP cc_start: 0.6393 (t0) cc_final: 0.6137 (t0) REVERT: F 1236 LEU cc_start: 0.7841 (mt) cc_final: 0.7455 (tp) REVERT: F 1260 ARG cc_start: 0.7552 (ttt-90) cc_final: 0.6839 (ptm160) REVERT: F 1289 ARG cc_start: 0.7294 (mtt180) cc_final: 0.7009 (mtm-85) REVERT: F 1320 PHE cc_start: 0.5564 (p90) cc_final: 0.5210 (p90) REVERT: F 1333 ARG cc_start: 0.7464 (ttm170) cc_final: 0.7261 (ttt180) outliers start: 27 outliers final: 11 residues processed: 239 average time/residue: 0.3696 time to fit residues: 131.2531 Evaluate side-chains 218 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 433 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain I residue 1320 PHE Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1221 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 83 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 214 optimal weight: 0.0670 chunk 80 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 200 optimal weight: 0.0020 chunk 59 optimal weight: 0.9980 overall best weight: 0.4326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 HIS ** I1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.117622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.083355 restraints weight = 48462.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081923 restraints weight = 28164.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.082683 restraints weight = 23615.022| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20838 Z= 0.119 Angle : 0.609 10.379 28298 Z= 0.313 Chirality : 0.045 0.225 3013 Planarity : 0.005 0.059 3657 Dihedral : 5.446 26.519 2742 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.18 % Allowed : 14.10 % Favored : 83.73 % 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: -1.44 (0.17), residues: 2508 helix: 0.51 (0.28), residues: 373 sheet: -1.31 (0.18), residues: 725 loop : -1.12 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 375 HIS 0.007 0.001 HIS D 742 PHE 0.014 0.001 PHE F1248 TYR 0.023 0.001 TYR F1251 ARG 0.007 0.000 ARG G1260 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 668) hydrogen bonds : angle 6.03940 ( 1779) covalent geometry : bond 0.00273 (20838) covalent geometry : angle 0.60863 (28298) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8190 (t0) cc_final: 0.7666 (t70) REVERT: A 771 MET cc_start: 0.7618 (mtt) cc_final: 0.7259 (mtt) REVERT: G 1251 TYR cc_start: 0.7136 (m-80) cc_final: 0.6639 (m-80) REVERT: G 1323 PHE cc_start: 0.7048 (t80) cc_final: 0.6686 (t80) REVERT: C 1260 ARG cc_start: 0.7636 (mtp180) cc_final: 0.7352 (ttt-90) REVERT: C 1268 MET cc_start: 0.4134 (mmp) cc_final: 0.3920 (mmt) REVERT: C 1272 PHE cc_start: 0.4457 (m-80) cc_final: 0.4094 (m-80) REVERT: D 251 ASP cc_start: 0.8079 (m-30) cc_final: 0.7679 (t0) REVERT: E 1096 ASN cc_start: 0.7327 (t0) cc_final: 0.6846 (t0) REVERT: E 1184 MET cc_start: 0.7556 (tmm) cc_final: 0.7292 (tmm) REVERT: I 1321 SER cc_start: 0.6921 (m) cc_final: 0.6408 (t) REVERT: I 1323 PHE cc_start: 0.6235 (t80) cc_final: 0.5901 (t80) REVERT: I 1338 ASP cc_start: 0.6524 (t0) cc_final: 0.6226 (t0) REVERT: I 1346 TRP cc_start: 0.5848 (t60) cc_final: 0.4954 (t60) REVERT: F 1236 LEU cc_start: 0.7786 (mt) cc_final: 0.7470 (tp) REVERT: F 1260 ARG cc_start: 0.7522 (ttt-90) cc_final: 0.6852 (ptm160) REVERT: F 1289 ARG cc_start: 0.7261 (mtt180) cc_final: 0.7015 (mtm-85) REVERT: F 1320 PHE cc_start: 0.6002 (p90) cc_final: 0.5799 (p90) outliers start: 48 outliers final: 25 residues processed: 263 average time/residue: 0.3486 time to fit residues: 137.2845 Evaluate side-chains 221 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain G residue 1292 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain I residue 1332 ILE Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1221 MET Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1241 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 28 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 88 optimal weight: 0.0270 chunk 128 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 228 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 210 optimal weight: 0.0020 overall best weight: 1.0050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.116440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082068 restraints weight = 48247.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.080624 restraints weight = 27358.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.082181 restraints weight = 20658.494| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20838 Z= 0.150 Angle : 0.613 8.355 28298 Z= 0.313 Chirality : 0.045 0.270 3013 Planarity : 0.005 0.068 3657 Dihedral : 5.289 23.879 2740 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.36 % Allowed : 14.78 % Favored : 82.86 % 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: -1.36 (0.17), residues: 2508 helix: 0.66 (0.28), residues: 373 sheet: -1.27 (0.18), residues: 739 loop : -1.08 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 375 HIS 0.004 0.001 HIS F1249 PHE 0.031 0.001 PHE E1182 TYR 0.015 0.001 TYR A 363 ARG 0.007 0.000 ARG G1260 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 668) hydrogen bonds : angle 5.90936 ( 1779) covalent geometry : bond 0.00349 (20838) covalent geometry : angle 0.61263 (28298) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8124 (t0) cc_final: 0.7567 (t70) REVERT: G 1323 PHE cc_start: 0.7050 (t80) cc_final: 0.6780 (t80) REVERT: C 1260 ARG cc_start: 0.7650 (mtp180) cc_final: 0.7381 (ttt-90) REVERT: D 251 ASP cc_start: 0.8084 (m-30) cc_final: 0.7658 (t0) REVERT: D 710 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7848 (mp10) REVERT: D 771 MET cc_start: 0.7489 (mtt) cc_final: 0.7238 (mtt) REVERT: E 1096 ASN cc_start: 0.7208 (t0) cc_final: 0.6762 (t0) REVERT: I 1321 SER cc_start: 0.6909 (m) cc_final: 0.6383 (t) REVERT: I 1338 ASP cc_start: 0.6574 (t0) cc_final: 0.6253 (t0) REVERT: I 1346 TRP cc_start: 0.5991 (t60) cc_final: 0.5190 (t60) REVERT: F 1236 LEU cc_start: 0.7777 (mt) cc_final: 0.7454 (tp) REVERT: F 1260 ARG cc_start: 0.7509 (ttt-90) cc_final: 0.6836 (ptm160) REVERT: F 1289 ARG cc_start: 0.7256 (mtt180) cc_final: 0.7036 (mtm-85) outliers start: 52 outliers final: 33 residues processed: 239 average time/residue: 0.3485 time to fit residues: 127.1705 Evaluate side-chains 220 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1203 HIS Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain G residue 1292 VAL Chi-restraints excluded: chain G residue 1350 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1273 VAL Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 433 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain E residue 1100 VAL Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1221 MET Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1241 VAL Chi-restraints excluded: chain F residue 1325 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.4166 > 50: distance: 33 - 105: 10.274 distance: 35 - 37: 5.326 distance: 36 - 102: 11.525 distance: 37 - 38: 15.511 distance: 38 - 39: 25.334 distance: 38 - 41: 3.025 distance: 39 - 40: 29.924 distance: 39 - 45: 32.299 distance: 41 - 42: 18.283 distance: 42 - 43: 9.266 distance: 43 - 44: 23.581 distance: 45 - 46: 37.101 distance: 45 - 51: 36.718 distance: 46 - 47: 5.144 distance: 46 - 49: 23.778 distance: 47 - 48: 7.339 distance: 47 - 52: 13.735 distance: 49 - 50: 22.223 distance: 50 - 51: 28.194 distance: 52 - 53: 11.288 distance: 53 - 54: 7.564 distance: 53 - 56: 7.135 distance: 54 - 55: 21.710 distance: 54 - 64: 26.615 distance: 56 - 57: 16.385 distance: 57 - 58: 23.697 distance: 57 - 59: 16.705 distance: 58 - 60: 18.971 distance: 59 - 61: 27.477 distance: 60 - 62: 24.399 distance: 61 - 62: 12.486 distance: 62 - 63: 10.567 distance: 64 - 65: 39.325 distance: 65 - 66: 10.576 distance: 66 - 67: 20.090 distance: 66 - 68: 10.269 distance: 68 - 69: 10.475 distance: 69 - 70: 11.564 distance: 69 - 72: 12.048 distance: 70 - 71: 18.230 distance: 70 - 74: 12.310 distance: 72 - 73: 20.822 distance: 74 - 75: 12.143 distance: 75 - 76: 9.977 distance: 75 - 78: 16.292 distance: 76 - 77: 13.766 distance: 76 - 85: 11.637 distance: 78 - 79: 17.914 distance: 79 - 80: 9.728 distance: 80 - 81: 4.835 distance: 81 - 82: 10.054 distance: 82 - 83: 4.546 distance: 82 - 84: 8.689 distance: 85 - 86: 4.298 distance: 86 - 87: 5.532 distance: 86 - 89: 7.133 distance: 87 - 88: 10.639 distance: 87 - 94: 13.820 distance: 89 - 90: 6.991 distance: 90 - 91: 6.380 distance: 91 - 92: 5.227 distance: 91 - 93: 4.199 distance: 94 - 95: 9.022 distance: 95 - 96: 9.670 distance: 95 - 98: 12.032 distance: 96 - 97: 14.513 distance: 96 - 102: 7.161 distance: 98 - 99: 9.113 distance: 99 - 100: 11.611 distance: 99 - 101: 12.180 distance: 102 - 103: 4.348 distance: 103 - 104: 9.442 distance: 104 - 105: 18.464 distance: 104 - 108: 13.403 distance: 106 - 107: 5.077 distance: 108 - 109: 6.820 distance: 109 - 110: 7.077 distance: 109 - 112: 6.227 distance: 110 - 111: 10.003 distance: 112 - 113: 16.754 distance: 113 - 114: 16.642 distance: 113 - 115: 15.409