Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 20:44:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3o_17387/08_2023/8p3o_17387.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3o_17387/08_2023/8p3o_17387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3o_17387/08_2023/8p3o_17387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3o_17387/08_2023/8p3o_17387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3o_17387/08_2023/8p3o_17387.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3o_17387/08_2023/8p3o_17387.pdb" } resolution = 2.9 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= 0.027 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 120 5.16 5 C 13392 2.51 5 N 3776 2.21 5 O 3904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 85": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 83": "OD1" <-> "OD2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 21192 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "B" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "C" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "G" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "A" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "F" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "H" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Time building chain proxies: 9.92, per 1000 atoms: 0.47 Number of scatterers: 21192 At special positions: 0 Unit cell: (131.008, 131.008, 172.652, 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 120 16.00 O 3904 8.00 N 3776 7.00 C 13392 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: 8.56 Conformation dependent library (CDL) restraints added in 3.0 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 8 sheets defined 67.7% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'D' and resid 18 through 29 removed outlier: 3.660A pdb=" N ARG D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 29 " --> pdb=" O THR D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 49 removed outlier: 3.644A pdb=" N ILE D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 removed outlier: 3.574A pdb=" N GLN D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 82 " --> pdb=" O PHE D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 110 through 120 removed outlier: 3.545A pdb=" N TRP D 118 " --> pdb=" O ARG D 114 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.749A pdb=" N ASN D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 238 removed outlier: 3.556A pdb=" N LEU D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 209 " --> pdb=" O MET D 205 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 removed outlier: 3.520A pdb=" N LEU D 251 " --> pdb=" O ALA D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 275 Processing helix chain 'D' and resid 279 through 295 removed outlier: 3.854A pdb=" N ASP D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 348 Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 49 removed outlier: 3.716A pdb=" N ILE B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 removed outlier: 3.576A pdb=" N GLN B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 82 " --> pdb=" O PHE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 110 through 120 removed outlier: 3.546A pdb=" N TRP B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 131 through 144 removed outlier: 3.522A pdb=" N ALA B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 238 removed outlier: 3.554A pdb=" N LEU B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 176 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 209 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.513A pdb=" N LEU B 251 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.839A pdb=" N ASP B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 348 Processing helix chain 'C' and resid 18 through 29 removed outlier: 3.799A pdb=" N ARG C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP C 27 " --> pdb=" O PHE C 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 28 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 29 " --> pdb=" O THR C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 48 removed outlier: 4.215A pdb=" N ILE C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 removed outlier: 3.751A pdb=" N GLN C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 109 Processing helix chain 'C' and resid 110 through 119 removed outlier: 3.512A pdb=" N ARG C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.521A pdb=" N ASN C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 235 removed outlier: 3.888A pdb=" N ASN C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 260 through 273 removed outlier: 3.743A pdb=" N LEU C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 295 removed outlier: 3.794A pdb=" N ASP C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY C 295 " --> pdb=" O THR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 348 removed outlier: 4.157A pdb=" N LEU C 325 " --> pdb=" O ARG C 321 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYS C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 29 removed outlier: 3.705A pdb=" N ARG G 24 " --> pdb=" O ARG G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.860A pdb=" N ILE G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU G 38 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA G 39 " --> pdb=" O GLY G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 removed outlier: 3.752A pdb=" N GLN G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 109 Processing helix chain 'G' and resid 110 through 119 removed outlier: 3.545A pdb=" N ARG G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU G 119 " --> pdb=" O ARG G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.544A pdb=" N ASN G 144 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 235 removed outlier: 3.885A pdb=" N ASN G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS G 210 " --> pdb=" O LYS G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 249 Processing helix chain 'G' and resid 260 through 273 removed outlier: 3.743A pdb=" N LEU G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 295 removed outlier: 3.795A pdb=" N ASP G 283 " --> pdb=" O ASP G 279 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR G 291 " --> pdb=" O ALA G 287 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY G 295 " --> pdb=" O THR G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 348 removed outlier: 4.238A pdb=" N LEU G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET G 326 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE G 327 " --> pdb=" O ALA G 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 29 removed outlier: 3.745A pdb=" N GLY A 29 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 43 removed outlier: 3.773A pdb=" N ILE A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 71 through 86 removed outlier: 3.749A pdb=" N GLN A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 109 Processing helix chain 'A' and resid 110 through 119 removed outlier: 3.512A pdb=" N ARG A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.541A pdb=" N ASN A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 235 removed outlier: 3.890A pdb=" N ASN A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.742A pdb=" N LEU A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.795A pdb=" N ASP A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 348 Processing helix chain 'F' and resid 18 through 29 removed outlier: 3.595A pdb=" N ARG F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 49 removed outlier: 4.172A pdb=" N ILE F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU F 38 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 84 removed outlier: 3.572A pdb=" N GLN F 75 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 110 Processing helix chain 'F' and resid 110 through 120 removed outlier: 3.546A pdb=" N TRP F 118 " --> pdb=" O ARG F 114 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.747A pdb=" N ASN F 144 " --> pdb=" O ASP F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 238 removed outlier: 3.555A pdb=" N LEU F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN F 208 " --> pdb=" O GLN F 204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL F 209 " --> pdb=" O MET F 205 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS F 210 " --> pdb=" O LYS F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.501A pdb=" N LEU F 251 " --> pdb=" O ALA F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 275 Processing helix chain 'F' and resid 279 through 295 removed outlier: 3.840A pdb=" N ASP F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR F 291 " --> pdb=" O ALA F 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY F 295 " --> pdb=" O THR F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 348 removed outlier: 3.504A pdb=" N LEU F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 removed outlier: 3.558A pdb=" N ARG H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 49 removed outlier: 3.749A pdb=" N ILE H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE H 49 " --> pdb=" O LEU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 86 removed outlier: 3.574A pdb=" N GLN H 75 " --> pdb=" O GLY H 71 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU H 82 " --> pdb=" O PHE H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 110 Processing helix chain 'H' and resid 110 through 120 removed outlier: 3.546A pdb=" N TRP H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 119 " --> pdb=" O ARG H 115 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.749A pdb=" N ASN H 144 " --> pdb=" O ASP H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 238 removed outlier: 3.555A pdb=" N LEU H 175 " --> pdb=" O ALA H 171 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG H 176 " --> pdb=" O ASN H 172 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN H 208 " --> pdb=" O GLN H 204 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL H 209 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS H 210 " --> pdb=" O LYS H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 251 removed outlier: 3.512A pdb=" N LEU H 251 " --> pdb=" O ALA H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 275 Processing helix chain 'H' and resid 279 through 295 removed outlier: 3.875A pdb=" N ASP H 283 " --> pdb=" O ASP H 279 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR H 291 " --> pdb=" O ALA H 287 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL H 294 " --> pdb=" O ASN H 290 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY H 295 " --> pdb=" O THR H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 348 Processing helix chain 'E' and resid 18 through 29 removed outlier: 3.551A pdb=" N ARG E 24 " --> pdb=" O ARG E 20 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY E 29 " --> pdb=" O THR E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.629A pdb=" N MET E 36 " --> pdb=" O TRP E 32 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA E 44 " --> pdb=" O PHE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.751A pdb=" N GLN E 75 " --> pdb=" O GLY E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 109 Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.545A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 119 " --> pdb=" O ARG E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.536A pdb=" N ASN E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 235 removed outlier: 3.889A pdb=" N ASN E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E 210 " --> pdb=" O LYS E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 261 through 273 Processing helix chain 'E' and resid 279 through 295 removed outlier: 3.794A pdb=" N ASP E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY E 295 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 348 removed outlier: 4.023A pdb=" N LEU E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 146 through 149 removed outlier: 6.109A pdb=" N ILE D 60 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 146 through 149 removed outlier: 6.108A pdb=" N ILE B 60 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 146 through 149 removed outlier: 6.100A pdb=" N ILE C 60 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 146 through 149 removed outlier: 6.081A pdb=" N ILE G 60 " --> pdb=" O LEU G 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 149 removed outlier: 6.098A pdb=" N ILE A 60 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 146 through 149 removed outlier: 6.107A pdb=" N ILE F 60 " --> pdb=" O LEU F 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 146 through 149 removed outlier: 6.107A pdb=" N ILE H 60 " --> pdb=" O LEU H 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 146 through 149 removed outlier: 6.100A pdb=" N ILE E 60 " --> pdb=" O LEU E 308 " (cutoff:3.500A) 1378 hydrogen bonds defined for protein. 4020 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: 6.82 Time building geometry restraints manager: 8.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7094 1.34 - 1.46: 3667 1.46 - 1.58: 10623 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 21616 Sorted by residual: bond pdb=" N VAL H 84 " pdb=" CA VAL H 84 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.32e-02 5.74e+03 8.47e+00 bond pdb=" N VAL B 84 " pdb=" CA VAL B 84 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.32e-02 5.74e+03 7.94e+00 bond pdb=" CA ARG F 85 " pdb=" C ARG F 85 " ideal model delta sigma weight residual 1.520 1.559 -0.038 1.39e-02 5.18e+03 7.64e+00 bond pdb=" N VAL F 84 " pdb=" CA VAL F 84 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.29e-02 6.01e+03 7.25e+00 bond pdb=" N VAL D 84 " pdb=" CA VAL D 84 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.89e+00 ... (remaining 21611 not shown) Histogram of bond angle deviations from ideal: 97.72 - 105.02: 406 105.02 - 112.32: 10373 112.32 - 119.62: 7587 119.62 - 126.92: 10613 126.92 - 134.22: 277 Bond angle restraints: 29256 Sorted by residual: angle pdb=" N ASP H 83 " pdb=" CA ASP H 83 " pdb=" C ASP H 83 " ideal model delta sigma weight residual 113.18 108.33 4.85 1.21e+00 6.83e-01 1.61e+01 angle pdb=" N ASP B 83 " pdb=" CA ASP B 83 " pdb=" C ASP B 83 " ideal model delta sigma weight residual 113.18 108.39 4.79 1.21e+00 6.83e-01 1.57e+01 angle pdb=" CA SER F 86 " pdb=" C SER F 86 " pdb=" O SER F 86 " ideal model delta sigma weight residual 121.68 117.06 4.62 1.18e+00 7.18e-01 1.53e+01 angle pdb=" N PRO F 262 " pdb=" CA PRO F 262 " pdb=" C PRO F 262 " ideal model delta sigma weight residual 113.40 108.28 5.12 1.34e+00 5.57e-01 1.46e+01 angle pdb=" N PRO D 262 " pdb=" CA PRO D 262 " pdb=" C PRO D 262 " ideal model delta sigma weight residual 113.40 108.32 5.08 1.34e+00 5.57e-01 1.44e+01 ... (remaining 29251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 11203 17.58 - 35.15: 1427 35.15 - 52.73: 372 52.73 - 70.31: 101 70.31 - 87.88: 25 Dihedral angle restraints: 13128 sinusoidal: 5352 harmonic: 7776 Sorted by residual: dihedral pdb=" CA GLU D 255 " pdb=" C GLU D 255 " pdb=" N MET D 256 " pdb=" CA MET D 256 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA SER H 254 " pdb=" C SER H 254 " pdb=" N GLU H 255 " pdb=" CA GLU H 255 " ideal model delta harmonic sigma weight residual -180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA SER B 254 " pdb=" C SER B 254 " pdb=" N GLU B 255 " pdb=" CA GLU B 255 " ideal model delta harmonic sigma weight residual 180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 13125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2695 0.051 - 0.101: 392 0.101 - 0.152: 77 0.152 - 0.202: 9 0.202 - 0.253: 11 Chirality restraints: 3184 Sorted by residual: chirality pdb=" CG LEU G 26 " pdb=" CB LEU G 26 " pdb=" CD1 LEU G 26 " pdb=" CD2 LEU G 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA SER H 160 " pdb=" N SER H 160 " pdb=" C SER H 160 " pdb=" CB SER H 160 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA SER B 160 " pdb=" N SER B 160 " pdb=" C SER B 160 " pdb=" CB SER B 160 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 3181 not shown) Planarity restraints: 3832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 85 " 0.229 9.50e-02 1.11e+02 1.03e-01 6.46e+00 pdb=" NE ARG B 85 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 85 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 85 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 85 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 324 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C PHE G 324 " -0.044 2.00e-02 2.50e+03 pdb=" O PHE G 324 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU G 325 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 153 " -0.010 2.00e-02 2.50e+03 1.23e-02 2.66e+00 pdb=" CG PHE C 153 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 153 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 153 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 153 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 153 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 153 " -0.000 2.00e-02 2.50e+03 ... (remaining 3829 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1915 2.74 - 3.28: 20837 3.28 - 3.82: 33214 3.82 - 4.36: 37184 4.36 - 4.90: 65071 Nonbonded interactions: 158221 Sorted by model distance: nonbonded pdb=" ND2 ASN A 270 " pdb=" O SER H 254 " model vdw 2.204 2.520 nonbonded pdb=" O LEU G 22 " pdb=" OG1 THR G 25 " model vdw 2.217 2.440 nonbonded pdb=" O LEU H 45 " pdb=" OG1 THR H 48 " model vdw 2.225 2.440 nonbonded pdb=" O LEU D 45 " pdb=" OG1 THR D 48 " model vdw 2.229 2.440 nonbonded pdb=" O LEU C 45 " pdb=" OG1 THR C 48 " model vdw 2.231 2.440 ... (remaining 158216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 6.580 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: 22.760 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 52.160 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 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 0.043 21616 Z= 0.187 Angle : 0.721 11.032 29256 Z= 0.379 Chirality : 0.041 0.253 3184 Planarity : 0.004 0.103 3832 Dihedral : 17.208 87.883 8088 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.02 (0.16), residues: 2640 helix: 1.51 (0.12), residues: 1660 sheet: 0.91 (0.44), residues: 200 loop : -1.21 (0.21), residues: 780 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 0 residues processed: 175 average time/residue: 1.6822 time to fit residues: 326.5392 Evaluate side-chains 143 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN G 75 GLN A 75 GLN E 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.031 21616 Z= 0.402 Angle : 0.657 9.864 29256 Z= 0.348 Chirality : 0.040 0.181 3184 Planarity : 0.004 0.040 3832 Dihedral : 3.955 18.523 2952 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.25 (0.17), residues: 2640 helix: 2.75 (0.12), residues: 1680 sheet: 0.87 (0.44), residues: 200 loop : -1.36 (0.21), residues: 760 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 152 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 13 residues processed: 203 average time/residue: 1.6034 time to fit residues: 363.5684 Evaluate side-chains 161 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 2.527 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 1.1923 time to fit residues: 8.8172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 199 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 66 optimal weight: 40.0000 chunk 240 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 213 optimal weight: 0.1980 chunk 238 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN B 75 GLN H 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 21616 Z= 0.172 Angle : 0.573 10.840 29256 Z= 0.289 Chirality : 0.036 0.145 3184 Planarity : 0.003 0.039 3832 Dihedral : 3.741 19.969 2952 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.60 (0.17), residues: 2640 helix: 3.09 (0.12), residues: 1656 sheet: 1.06 (0.43), residues: 216 loop : -1.34 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 148 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 10 residues processed: 191 average time/residue: 1.6209 time to fit residues: 346.9150 Evaluate side-chains 155 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 2.566 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.8813 time to fit residues: 5.3337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 161 optimal weight: 0.0870 chunk 241 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 87 ASN F 75 GLN F 81 ASN H 75 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 21616 Z= 0.210 Angle : 0.588 11.885 29256 Z= 0.292 Chirality : 0.036 0.140 3184 Planarity : 0.003 0.027 3832 Dihedral : 3.672 19.120 2952 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.84 (0.17), residues: 2640 helix: 3.37 (0.12), residues: 1628 sheet: 1.16 (0.43), residues: 216 loop : -1.30 (0.21), residues: 796 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 179 average time/residue: 1.5692 time to fit residues: 316.0552 Evaluate side-chains 157 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 2.530 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 1.1911 time to fit residues: 7.4571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 217 optimal weight: 0.3980 chunk 176 optimal weight: 0.4980 chunk 0 optimal weight: 50.0000 chunk 130 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN D 236 GLN B 75 GLN B 236 GLN A 87 ASN F 75 GLN F 81 ASN H 236 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 21616 Z= 0.294 Angle : 0.611 9.704 29256 Z= 0.308 Chirality : 0.038 0.148 3184 Planarity : 0.003 0.027 3832 Dihedral : 3.756 19.138 2952 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.66 (0.17), residues: 2640 helix: 3.14 (0.12), residues: 1688 sheet: 1.05 (0.43), residues: 216 loop : -1.55 (0.22), residues: 736 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 143 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 24 residues processed: 178 average time/residue: 1.4441 time to fit residues: 290.4835 Evaluate side-chains 166 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 2.539 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 1.1971 time to fit residues: 8.6966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN D 237 HIS A 87 ASN F 75 GLN F 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 21616 Z= 0.238 Angle : 0.608 9.425 29256 Z= 0.300 Chirality : 0.037 0.152 3184 Planarity : 0.003 0.027 3832 Dihedral : 3.700 18.932 2952 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.76 (0.17), residues: 2640 helix: 3.28 (0.12), residues: 1660 sheet: 1.13 (0.43), residues: 216 loop : -1.50 (0.21), residues: 764 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 146 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 26 residues processed: 192 average time/residue: 1.4138 time to fit residues: 308.1941 Evaluate side-chains 172 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 2.507 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 5 average time/residue: 1.0586 time to fit residues: 9.4660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 254 optimal weight: 0.0040 chunk 159 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN D 81 ASN B 81 ASN C 87 ASN G 87 ASN F 75 GLN H 81 ASN E 87 ASN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 21616 Z= 0.167 Angle : 0.605 10.211 29256 Z= 0.292 Chirality : 0.036 0.153 3184 Planarity : 0.003 0.026 3832 Dihedral : 3.619 19.724 2952 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.90 (0.17), residues: 2640 helix: 3.35 (0.12), residues: 1656 sheet: 1.29 (0.43), residues: 216 loop : -1.32 (0.22), residues: 768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 148 time to evaluate : 2.437 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 20 residues processed: 188 average time/residue: 1.5313 time to fit residues: 324.6708 Evaluate side-chains 161 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 2.625 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.7711 time to fit residues: 5.1341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 231 optimal weight: 40.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN D 81 ASN B 81 ASN C 87 ASN G 87 ASN H 81 ASN E 87 ASN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 21616 Z= 0.317 Angle : 0.669 11.902 29256 Z= 0.327 Chirality : 0.038 0.157 3184 Planarity : 0.003 0.026 3832 Dihedral : 3.754 18.037 2952 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.73 (0.17), residues: 2640 helix: 3.26 (0.12), residues: 1668 sheet: 1.08 (0.43), residues: 216 loop : -1.55 (0.22), residues: 756 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 143 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 24 residues processed: 179 average time/residue: 1.4543 time to fit residues: 294.3353 Evaluate side-chains 168 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 2.310 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 2 average time/residue: 1.2299 time to fit residues: 6.0670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 142 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 224 optimal weight: 0.9990 chunk 236 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN D 81 ASN B 81 ASN C 87 ASN G 87 ASN H 75 GLN H 81 ASN E 87 ASN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 21616 Z= 0.175 Angle : 0.655 12.237 29256 Z= 0.313 Chirality : 0.037 0.154 3184 Planarity : 0.003 0.042 3832 Dihedral : 3.644 19.663 2952 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.88 (0.17), residues: 2640 helix: 3.41 (0.12), residues: 1640 sheet: 1.24 (0.43), residues: 216 loop : -1.42 (0.21), residues: 784 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 2.332 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 175 average time/residue: 1.4833 time to fit residues: 292.8590 Evaluate side-chains 165 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 2.363 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 1 average time/residue: 0.3982 time to fit residues: 3.7489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 128 optimal weight: 0.0070 chunk 166 optimal weight: 20.0000 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN B 75 GLN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 21616 Z= 0.182 Angle : 0.679 12.750 29256 Z= 0.320 Chirality : 0.037 0.178 3184 Planarity : 0.003 0.042 3832 Dihedral : 3.600 18.872 2952 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.88 (0.17), residues: 2640 helix: 3.31 (0.12), residues: 1660 sheet: 1.30 (0.43), residues: 216 loop : -1.31 (0.22), residues: 764 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 22 residues processed: 166 average time/residue: 1.5349 time to fit residues: 286.3823 Evaluate side-chains 164 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 2.198 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 0 time to fit residues: 3.2749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 193 optimal weight: 0.0570 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 184 optimal weight: 0.3980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.077052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.048690 restraints weight = 93002.058| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.97 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 21616 Z= 0.169 Angle : 0.677 12.816 29256 Z= 0.317 Chirality : 0.036 0.145 3184 Planarity : 0.003 0.040 3832 Dihedral : 3.542 18.944 2952 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.93 (0.17), residues: 2640 helix: 3.34 (0.12), residues: 1664 sheet: 1.39 (0.43), residues: 216 loop : -1.32 (0.22), residues: 760 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6206.09 seconds wall clock time: 111 minutes 46.01 seconds (6706.01 seconds total)