Starting phenix.real_space_refine on Thu Apr 11 02:03:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3o_17387/04_2024/8p3o_17387.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3o_17387/04_2024/8p3o_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_17387/04_2024/8p3o_17387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3o_17387/04_2024/8p3o_17387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3o_17387/04_2024/8p3o_17387.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3o_17387/04_2024/8p3o_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-dev-5288/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: 11.59, per 1000 atoms: 0.55 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: 7.84 Conformation dependent library (CDL) restraints added in 3.7 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: 1.67 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: 6.57 Time building geometry restraints manager: 8.64 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: 10.460 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: 0.000 Extract box with map and model: 21.050 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 54.110 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.150 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:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.930 ------------------------------------------------------------------------------- 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 % Allowed : 26.77 % Favored : 72.82 % 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: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 329 HIS 0.002 0.000 HIS C 237 PHE 0.028 0.001 PHE C 153 TYR 0.011 0.001 TYR G 124 ARG 0.009 0.000 ARG E 241 *********************** 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 : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 68 MET cc_start: 0.9218 (pmm) cc_final: 0.9018 (pmt) REVERT: D 256 MET cc_start: 0.9370 (mpp) cc_final: 0.9164 (mpp) REVERT: B 140 ASP cc_start: 0.9444 (t0) cc_final: 0.9197 (t0) REVERT: C 97 MET cc_start: 0.9423 (mpp) cc_final: 0.9134 (mpp) REVERT: C 155 ARG cc_start: 0.9380 (ttm-80) cc_final: 0.9153 (mtm110) REVERT: G 36 MET cc_start: 0.8103 (pp-130) cc_final: 0.7609 (ppp) REVERT: G 42 LEU cc_start: 0.9312 (tm) cc_final: 0.8844 (pp) REVERT: A 42 LEU cc_start: 0.9228 (tm) cc_final: 0.8742 (pp) REVERT: F 140 ASP cc_start: 0.9446 (t0) cc_final: 0.9243 (t0) REVERT: H 36 MET cc_start: 0.7978 (ppp) cc_final: 0.7721 (pp-130) REVERT: H 40 PHE cc_start: 0.9354 (m-80) cc_final: 0.8838 (m-10) REVERT: H 155 ARG cc_start: 0.9375 (mtm-85) cc_final: 0.9150 (mtm110) REVERT: H 256 MET cc_start: 0.9359 (mpp) cc_final: 0.9119 (mpp) outliers start: 9 outliers final: 0 residues processed: 175 average time/residue: 1.7162 time to fit residues: 332.9304 Evaluate side-chains 147 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.574 ------------------------------------------------------------------------------- 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: 0.9980 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 134 optimal weight: 0.0470 chunk 106 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- 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: 0.8666 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21616 Z= 0.268 Angle : 0.609 10.536 29256 Z= 0.319 Chirality : 0.038 0.179 3184 Planarity : 0.004 0.035 3832 Dihedral : 3.827 18.755 2952 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.41 % Allowed : 23.68 % Favored : 73.91 % 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: 2.31 (0.17), residues: 2640 helix: 2.80 (0.12), residues: 1676 sheet: 0.77 (0.43), residues: 216 loop : -1.34 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 32 HIS 0.002 0.001 HIS G 237 PHE 0.020 0.001 PHE A 153 TYR 0.013 0.002 TYR G 47 ARG 0.009 0.000 ARG F 85 *********************** 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 206 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 153 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 256 MET cc_start: 0.9296 (mpp) cc_final: 0.8853 (mpp) REVERT: B 140 ASP cc_start: 0.9457 (t0) cc_final: 0.9140 (t0) REVERT: B 256 MET cc_start: 0.9121 (mpp) cc_final: 0.8829 (mpp) REVERT: G 36 MET cc_start: 0.8060 (pp-130) cc_final: 0.7466 (ppp) REVERT: A 26 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9006 (pp) REVERT: A 42 LEU cc_start: 0.9228 (tm) cc_final: 0.8802 (pp) REVERT: F 140 ASP cc_start: 0.9452 (t0) cc_final: 0.9184 (t0) REVERT: F 256 MET cc_start: 0.9151 (mpp) cc_final: 0.8876 (mpp) REVERT: H 40 PHE cc_start: 0.9343 (m-80) cc_final: 0.8866 (m-10) REVERT: H 256 MET cc_start: 0.9267 (mpp) cc_final: 0.8746 (mpp) outliers start: 53 outliers final: 4 residues processed: 197 average time/residue: 1.6490 time to fit residues: 361.5498 Evaluate side-chains 151 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain H residue 226 SER 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: 9.9990 chunk 163 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 238 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2288 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= 0.193 Angle : 0.561 10.640 29256 Z= 0.285 Chirality : 0.036 0.145 3184 Planarity : 0.003 0.041 3832 Dihedral : 3.657 18.214 2952 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.95 % Allowed : 23.82 % Favored : 74.23 % 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: 2.59 (0.17), residues: 2640 helix: 3.04 (0.12), residues: 1680 sheet: 1.08 (0.44), residues: 216 loop : -1.41 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 111 HIS 0.006 0.001 HIS G 237 PHE 0.017 0.001 PHE G 23 TYR 0.011 0.001 TYR E 123 ARG 0.007 0.000 ARG D 63 *********************** 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 190 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 147 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 256 MET cc_start: 0.9208 (mpp) cc_final: 0.8662 (mpp) REVERT: B 140 ASP cc_start: 0.9457 (t0) cc_final: 0.9159 (t0) REVERT: B 256 MET cc_start: 0.9024 (mpp) cc_final: 0.8661 (mpp) REVERT: G 36 MET cc_start: 0.7902 (pp-130) cc_final: 0.7319 (ppp) REVERT: A 42 LEU cc_start: 0.9287 (tm) cc_final: 0.8810 (pp) REVERT: F 140 ASP cc_start: 0.9446 (t0) cc_final: 0.9173 (t0) REVERT: F 256 MET cc_start: 0.9150 (mpp) cc_final: 0.8696 (mpp) REVERT: H 36 MET cc_start: 0.8134 (ppp) cc_final: 0.7927 (ppp) REVERT: H 40 PHE cc_start: 0.9293 (m-80) cc_final: 0.8813 (m-10) REVERT: H 256 MET cc_start: 0.9257 (mpp) cc_final: 0.8713 (mpp) outliers start: 43 outliers final: 3 residues processed: 183 average time/residue: 1.6683 time to fit residues: 340.0046 Evaluate side-chains 148 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 145 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain E residue 342 LEU 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: 4.9990 chunk 124 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 255 optimal weight: 0.0870 chunk 125 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- 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 B 81 ASN C 87 ASN A 87 ASN F 75 GLN F 81 ASN H 75 GLN H 81 ASN E 87 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2601 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= 0.188 Angle : 0.568 11.829 29256 Z= 0.282 Chirality : 0.036 0.139 3184 Planarity : 0.003 0.027 3832 Dihedral : 3.580 16.991 2952 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.55 % Allowed : 24.41 % Favored : 74.05 % 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: 2.89 (0.17), residues: 2640 helix: 3.40 (0.12), residues: 1628 sheet: 1.16 (0.43), residues: 216 loop : -1.27 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 111 HIS 0.001 0.000 HIS C 237 PHE 0.021 0.001 PHE A 153 TYR 0.014 0.001 TYR E 47 ARG 0.006 0.000 ARG B 63 *********************** 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 183 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 256 MET cc_start: 0.9239 (mpp) cc_final: 0.8778 (mpp) REVERT: B 140 ASP cc_start: 0.9461 (t0) cc_final: 0.9182 (t0) REVERT: B 256 MET cc_start: 0.9049 (mpp) cc_final: 0.8689 (mpp) REVERT: C 342 LEU cc_start: 0.4147 (OUTLIER) cc_final: 0.3786 (mm) REVERT: G 36 MET cc_start: 0.7765 (pp-130) cc_final: 0.7171 (ppp) REVERT: G 42 LEU cc_start: 0.9357 (tm) cc_final: 0.8876 (pp) REVERT: A 42 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8808 (pp) REVERT: F 140 ASP cc_start: 0.9453 (t0) cc_final: 0.9187 (t0) REVERT: F 256 MET cc_start: 0.9153 (mpp) cc_final: 0.8688 (mpp) REVERT: H 36 MET cc_start: 0.7905 (ppp) cc_final: 0.7601 (ppp) REVERT: H 40 PHE cc_start: 0.9275 (m-80) cc_final: 0.8752 (m-10) REVERT: H 256 MET cc_start: 0.9244 (mpp) cc_final: 0.8783 (mpp) REVERT: E 23 PHE cc_start: 0.4623 (OUTLIER) cc_final: 0.4359 (p90) outliers start: 34 outliers final: 8 residues processed: 175 average time/residue: 1.6066 time to fit residues: 314.3104 Evaluate side-chains 155 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.0870 chunk 144 optimal weight: 0.0770 chunk 3 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 217 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 130 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 overall best weight: 1.4118 ------------------------------------------------------------------------------- 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 81 ASN B 236 GLN C 87 ASN F 75 GLN H 81 ASN H 236 GLN E 87 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2690 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= 0.202 Angle : 0.570 9.808 29256 Z= 0.283 Chirality : 0.036 0.153 3184 Planarity : 0.003 0.026 3832 Dihedral : 3.558 16.675 2952 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.45 % Allowed : 24.55 % Favored : 74.00 % 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: 2.93 (0.17), residues: 2640 helix: 3.45 (0.12), residues: 1628 sheet: 1.13 (0.43), residues: 216 loop : -1.27 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 329 HIS 0.002 0.000 HIS A 237 PHE 0.013 0.001 PHE B 181 TYR 0.016 0.001 TYR E 47 ARG 0.004 0.000 ARG H 63 *********************** 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 177 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 256 MET cc_start: 0.9257 (mpp) cc_final: 0.8718 (mpp) REVERT: B 140 ASP cc_start: 0.9463 (t0) cc_final: 0.9183 (t0) REVERT: B 256 MET cc_start: 0.9049 (mpp) cc_final: 0.8644 (mpp) REVERT: G 36 MET cc_start: 0.7698 (pp-130) cc_final: 0.7103 (ppp) REVERT: A 42 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8825 (pp) REVERT: F 140 ASP cc_start: 0.9460 (t0) cc_final: 0.9195 (t0) REVERT: F 256 MET cc_start: 0.9170 (mpp) cc_final: 0.8707 (mpp) REVERT: H 36 MET cc_start: 0.7896 (ppp) cc_final: 0.7597 (ppp) REVERT: H 40 PHE cc_start: 0.9276 (m-80) cc_final: 0.8752 (m-10) REVERT: H 256 MET cc_start: 0.9274 (mpp) cc_final: 0.8745 (mpp) REVERT: E 23 PHE cc_start: 0.4665 (OUTLIER) cc_final: 0.4456 (OUTLIER) outliers start: 32 outliers final: 12 residues processed: 174 average time/residue: 1.4722 time to fit residues: 286.2128 Evaluate side-chains 159 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.8980 chunk 229 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 255 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 134 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 75 GLN B 81 ASN C 87 ASN G 87 ASN F 75 GLN H 75 GLN H 81 ASN E 87 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21616 Z= 0.162 Angle : 0.577 9.725 29256 Z= 0.279 Chirality : 0.036 0.157 3184 Planarity : 0.003 0.025 3832 Dihedral : 3.474 16.405 2952 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.68 % Allowed : 24.36 % Favored : 73.95 % 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: 3.01 (0.17), residues: 2640 helix: 3.41 (0.12), residues: 1664 sheet: 1.20 (0.43), residues: 216 loop : -1.24 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 329 HIS 0.002 0.000 HIS A 237 PHE 0.031 0.001 PHE F 40 TYR 0.017 0.001 TYR E 47 ARG 0.003 0.000 ARG G 85 *********************** 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 186 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 149 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 237 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7693 (m90) REVERT: D 256 MET cc_start: 0.9224 (mpp) cc_final: 0.8436 (mpt) REVERT: B 140 ASP cc_start: 0.9445 (t0) cc_final: 0.9179 (t0) REVERT: B 237 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7640 (m90) REVERT: B 256 MET cc_start: 0.9102 (mpp) cc_final: 0.8743 (mpp) REVERT: G 36 MET cc_start: 0.7553 (pp-130) cc_final: 0.6940 (ppp) REVERT: G 42 LEU cc_start: 0.9337 (tm) cc_final: 0.8883 (pp) REVERT: A 42 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8814 (pp) REVERT: F 140 ASP cc_start: 0.9459 (t0) cc_final: 0.9182 (t0) REVERT: F 256 MET cc_start: 0.9160 (mpp) cc_final: 0.8703 (mpp) REVERT: H 36 MET cc_start: 0.7796 (ppp) cc_final: 0.7521 (ppp) REVERT: H 40 PHE cc_start: 0.9282 (m-80) cc_final: 0.8750 (m-10) REVERT: H 237 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7628 (m90) REVERT: H 256 MET cc_start: 0.9230 (mpp) cc_final: 0.8442 (mpt) REVERT: E 23 PHE cc_start: 0.4648 (OUTLIER) cc_final: 0.4427 (OUTLIER) outliers start: 37 outliers final: 15 residues processed: 181 average time/residue: 1.5375 time to fit residues: 311.0298 Evaluate side-chains 163 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 237 HIS Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 2.9990 chunk 28 optimal weight: 0.0270 chunk 145 optimal weight: 0.0980 chunk 186 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 254 optimal weight: 0.0470 chunk 159 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21616 Z= 0.151 Angle : 0.594 14.451 29256 Z= 0.280 Chirality : 0.035 0.139 3184 Planarity : 0.003 0.044 3832 Dihedral : 3.410 16.201 2952 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.14 % Allowed : 24.82 % Favored : 74.05 % 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: 3.08 (0.17), residues: 2640 helix: 3.44 (0.12), residues: 1676 sheet: 1.29 (0.44), residues: 216 loop : -1.24 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 329 HIS 0.006 0.001 HIS E 237 PHE 0.036 0.001 PHE F 40 TYR 0.016 0.001 TYR E 47 ARG 0.006 0.000 ARG E 241 *********************** 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 172 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 256 MET cc_start: 0.9139 (tpp) cc_final: 0.8454 (mpt) REVERT: B 140 ASP cc_start: 0.9443 (t0) cc_final: 0.9172 (t0) REVERT: B 256 MET cc_start: 0.9038 (mpp) cc_final: 0.8732 (mpp) REVERT: G 36 MET cc_start: 0.7430 (pp-130) cc_final: 0.6813 (ppp) REVERT: G 42 LEU cc_start: 0.9318 (tm) cc_final: 0.8835 (pp) REVERT: A 42 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8741 (pp) REVERT: F 140 ASP cc_start: 0.9428 (t0) cc_final: 0.9173 (t0) REVERT: F 256 MET cc_start: 0.9119 (mpp) cc_final: 0.8693 (mpp) REVERT: H 36 MET cc_start: 0.7839 (ppp) cc_final: 0.7552 (ppp) REVERT: H 40 PHE cc_start: 0.9215 (m-80) cc_final: 0.8693 (m-10) REVERT: H 256 MET cc_start: 0.9152 (tpp) cc_final: 0.8414 (mpt) REVERT: E 23 PHE cc_start: 0.4647 (OUTLIER) cc_final: 0.4366 (p90) outliers start: 25 outliers final: 13 residues processed: 167 average time/residue: 1.5716 time to fit residues: 294.0123 Evaluate side-chains 158 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 68 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 231 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3057 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= 0.233 Angle : 0.634 12.376 29256 Z= 0.304 Chirality : 0.037 0.172 3184 Planarity : 0.003 0.032 3832 Dihedral : 3.537 15.043 2952 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.14 % Allowed : 24.91 % Favored : 73.95 % 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: 2.98 (0.17), residues: 2640 helix: 3.45 (0.12), residues: 1672 sheet: 1.12 (0.43), residues: 216 loop : -1.45 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 111 HIS 0.003 0.001 HIS A 237 PHE 0.018 0.001 PHE F 40 TYR 0.014 0.001 TYR E 47 ARG 0.002 0.000 ARG E 241 *********************** 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 171 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 2.335 Fit side-chains revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9178 (m-80) cc_final: 0.8836 (m-80) REVERT: D 256 MET cc_start: 0.9196 (tpp) cc_final: 0.8445 (mpt) REVERT: B 140 ASP cc_start: 0.9486 (t0) cc_final: 0.9222 (t0) REVERT: B 256 MET cc_start: 0.9093 (mpp) cc_final: 0.8749 (mpp) REVERT: C 256 MET cc_start: 0.8897 (ppp) cc_final: 0.7989 (mtt) REVERT: G 23 PHE cc_start: 0.6260 (OUTLIER) cc_final: 0.5819 (p90) REVERT: G 36 MET cc_start: 0.7453 (pp-130) cc_final: 0.6832 (ppp) REVERT: G 42 LEU cc_start: 0.9359 (tm) cc_final: 0.8894 (pp) REVERT: A 42 LEU cc_start: 0.9252 (tm) cc_final: 0.8765 (pp) REVERT: A 256 MET cc_start: 0.8929 (ppp) cc_final: 0.7986 (mtt) REVERT: F 83 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8527 (p0) REVERT: F 140 ASP cc_start: 0.9487 (t0) cc_final: 0.9235 (t0) REVERT: F 256 MET cc_start: 0.9122 (mpp) cc_final: 0.8737 (mpp) REVERT: H 36 MET cc_start: 0.7843 (ppp) cc_final: 0.7549 (ppp) REVERT: H 40 PHE cc_start: 0.9209 (m-80) cc_final: 0.8672 (m-10) REVERT: H 256 MET cc_start: 0.9176 (tpp) cc_final: 0.8403 (mpt) REVERT: E 23 PHE cc_start: 0.4707 (OUTLIER) cc_final: 0.4477 (OUTLIER) REVERT: E 344 ARG cc_start: 0.3081 (OUTLIER) cc_final: 0.2372 (tpm170) outliers start: 25 outliers final: 11 residues processed: 166 average time/residue: 1.5150 time to fit residues: 281.9372 Evaluate side-chains 160 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 344 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 0.6980 chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3224 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= 0.169 Angle : 0.622 12.375 29256 Z= 0.294 Chirality : 0.036 0.164 3184 Planarity : 0.003 0.028 3832 Dihedral : 3.489 15.687 2952 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.14 % Allowed : 25.23 % Favored : 73.64 % 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: 3.03 (0.17), residues: 2640 helix: 3.44 (0.12), residues: 1664 sheet: 1.16 (0.43), residues: 216 loop : -1.24 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 329 HIS 0.001 0.000 HIS A 237 PHE 0.035 0.001 PHE F 40 TYR 0.028 0.001 TYR B 47 ARG 0.011 0.000 ARG A 85 *********************** 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 171 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 2.163 Fit side-chains revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9153 (m-80) cc_final: 0.8781 (m-80) REVERT: D 256 MET cc_start: 0.9160 (tpp) cc_final: 0.8418 (mpt) REVERT: B 140 ASP cc_start: 0.9461 (t0) cc_final: 0.9184 (t0) REVERT: B 256 MET cc_start: 0.9127 (mpp) cc_final: 0.8786 (mpp) REVERT: G 23 PHE cc_start: 0.6260 (OUTLIER) cc_final: 0.5817 (p90) REVERT: G 36 MET cc_start: 0.7529 (pp-130) cc_final: 0.6866 (ppp) REVERT: A 42 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8763 (pp) REVERT: F 83 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8527 (p0) REVERT: F 140 ASP cc_start: 0.9464 (t0) cc_final: 0.9203 (t0) REVERT: F 256 MET cc_start: 0.9140 (mpp) cc_final: 0.8740 (mpp) REVERT: F 263 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8889 (pmm) REVERT: F 264 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8959 (mm) REVERT: H 36 MET cc_start: 0.7806 (ppp) cc_final: 0.7546 (ppp) REVERT: H 40 PHE cc_start: 0.9149 (m-80) cc_final: 0.8603 (m-10) REVERT: H 256 MET cc_start: 0.9188 (tpp) cc_final: 0.8439 (mpt) REVERT: H 263 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8899 (pmm) REVERT: H 264 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8981 (mm) REVERT: E 23 PHE cc_start: 0.4770 (OUTLIER) cc_final: 0.4536 (OUTLIER) REVERT: E 344 ARG cc_start: 0.3098 (OUTLIER) cc_final: 0.2386 (tpm170) outliers start: 25 outliers final: 13 residues processed: 163 average time/residue: 1.5948 time to fit residues: 290.5026 Evaluate side-chains 166 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 344 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 263 optimal weight: 40.0000 chunk 242 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 166 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3330 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= 0.174 Angle : 0.646 12.773 29256 Z= 0.302 Chirality : 0.036 0.152 3184 Planarity : 0.003 0.041 3832 Dihedral : 3.459 16.012 2952 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.09 % Allowed : 25.32 % Favored : 73.59 % 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: 3.03 (0.17), residues: 2640 helix: 3.44 (0.12), residues: 1664 sheet: 1.17 (0.43), residues: 216 loop : -1.23 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 329 HIS 0.001 0.000 HIS F 237 PHE 0.018 0.001 PHE A 153 TYR 0.013 0.001 TYR E 47 ARG 0.006 0.000 ARG G 85 ********************** 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 170 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9117 (m-80) cc_final: 0.8768 (m-80) REVERT: D 68 MET cc_start: 0.9125 (pmm) cc_final: 0.8886 (pmt) REVERT: D 256 MET cc_start: 0.9139 (tpp) cc_final: 0.8395 (mpt) REVERT: B 140 ASP cc_start: 0.9469 (t0) cc_final: 0.9201 (t0) REVERT: B 256 MET cc_start: 0.9103 (mpp) cc_final: 0.8758 (mpp) REVERT: G 23 PHE cc_start: 0.6223 (OUTLIER) cc_final: 0.5777 (p90) REVERT: G 36 MET cc_start: 0.7447 (pp-130) cc_final: 0.6787 (ppp) REVERT: A 42 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8755 (pp) REVERT: F 83 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8473 (p0) REVERT: F 140 ASP cc_start: 0.9473 (t0) cc_final: 0.9212 (t0) REVERT: F 256 MET cc_start: 0.9132 (mpp) cc_final: 0.8750 (mpp) REVERT: H 36 MET cc_start: 0.7789 (ppp) cc_final: 0.7532 (ppp) REVERT: H 40 PHE cc_start: 0.9117 (m-80) cc_final: 0.8573 (m-10) REVERT: H 256 MET cc_start: 0.9153 (tpp) cc_final: 0.8427 (mpt) REVERT: H 264 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8996 (mm) REVERT: E 23 PHE cc_start: 0.4782 (OUTLIER) cc_final: 0.4546 (OUTLIER) REVERT: E 344 ARG cc_start: 0.3056 (OUTLIER) cc_final: 0.2333 (tpm170) outliers start: 24 outliers final: 12 residues processed: 166 average time/residue: 1.5727 time to fit residues: 292.1387 Evaluate side-chains 161 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 344 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 193 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.076583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.047796 restraints weight = 92723.204| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 5.11 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3320 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= 0.189 Angle : 0.658 13.253 29256 Z= 0.308 Chirality : 0.036 0.144 3184 Planarity : 0.003 0.033 3832 Dihedral : 3.496 16.627 2952 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.00 % Allowed : 25.45 % Favored : 73.55 % 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: 3.01 (0.17), residues: 2640 helix: 3.42 (0.12), residues: 1664 sheet: 1.13 (0.43), residues: 216 loop : -1.21 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 329 HIS 0.001 0.000 HIS A 237 PHE 0.035 0.001 PHE F 40 TYR 0.025 0.001 TYR B 47 ARG 0.008 0.000 ARG F 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6495.45 seconds wall clock time: 122 minutes 58.06 seconds (7378.06 seconds total)