Starting phenix.real_space_refine on Sat Mar 16 03:14:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzh_20959/03_2024/6uzh_20959.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzh_20959/03_2024/6uzh_20959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzh_20959/03_2024/6uzh_20959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzh_20959/03_2024/6uzh_20959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzh_20959/03_2024/6uzh_20959.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzh_20959/03_2024/6uzh_20959.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 42 5.16 5 C 8715 2.51 5 N 2373 2.21 5 O 2443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 67": "OD1" <-> "OD2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 213": "OD1" <-> "OD2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ASP 218": "OD1" <-> "OD2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 218": "OD1" <-> "OD2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 181": "OE1" <-> "OE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 262": "OD1" <-> "OD2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "G ASP 67": "OD1" <-> "OD2" Residue "G TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G ASP 218": "OD1" <-> "OD2" Residue "G GLU 227": "OE1" <-> "OE2" Residue "G PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 262": "OD1" <-> "OD2" Residue "G PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13573 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "B" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "C" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "D" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "E" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "F" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "G" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Time building chain proxies: 6.79, per 1000 atoms: 0.50 Number of scatterers: 13573 At special positions: 0 Unit cell: (98, 97, 130, 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 42 16.00 O 2443 8.00 N 2373 7.00 C 8715 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: 5.19 Conformation dependent library (CDL) restraints added in 2.3 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 54.4% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 27 through 60 removed outlier: 3.562A pdb=" N ILE A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 90 removed outlier: 3.635A pdb=" N GLY A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 111 Processing helix chain 'A' and resid 111 through 127 Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'B' and resid 32 through 60 removed outlier: 3.593A pdb=" N LEU B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 43 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 removed outlier: 3.673A pdb=" N GLY B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 111 Processing helix chain 'B' and resid 111 through 127 Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'C' and resid 28 through 59 removed outlier: 3.518A pdb=" N SER C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 90 removed outlier: 3.567A pdb=" N GLY C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 111 Processing helix chain 'C' and resid 111 through 127 Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'D' and resid 28 through 60 Processing helix chain 'D' and resid 63 through 90 removed outlier: 3.505A pdb=" N GLY D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 111 removed outlier: 3.646A pdb=" N ILE D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 127 Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 245 through 265 Processing helix chain 'E' and resid 28 through 59 Processing helix chain 'E' and resid 65 through 90 removed outlier: 3.645A pdb=" N GLY E 90 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 3.680A pdb=" N ALA E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 127 Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 245 through 265 Processing helix chain 'F' and resid 28 through 60 Processing helix chain 'F' and resid 62 through 87 Processing helix chain 'F' and resid 94 through 127 removed outlier: 3.531A pdb=" N ALA F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASN F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 245 through 265 Processing helix chain 'G' and resid 28 through 60 Processing helix chain 'G' and resid 62 through 90 removed outlier: 3.883A pdb=" N PHE G 68 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY G 90 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 111 Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 167 through 172 Processing helix chain 'G' and resid 197 through 212 Processing helix chain 'G' and resid 245 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 137 removed outlier: 6.859A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.683A pdb=" N ASN A 234 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 279 removed outlier: 7.597A pdb=" N MET B 273 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASP A 274 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE B 277 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS A 278 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N MET C 273 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASP B 274 " --> pdb=" O MET C 273 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C 275 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN B 276 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE C 277 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET D 273 " --> pdb=" O GLN C 272 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP C 274 " --> pdb=" O MET D 273 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL D 275 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN C 276 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE D 277 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET E 273 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP D 274 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL E 275 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN D 276 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE E 277 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS D 278 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET F 273 " --> pdb=" O GLN E 272 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASP E 274 " --> pdb=" O MET F 273 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL F 275 " --> pdb=" O ASP E 274 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ASN E 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE F 277 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N MET G 273 " --> pdb=" O GLN F 272 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP F 274 " --> pdb=" O MET G 273 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL G 275 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N PHE G 277 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS F 278 " --> pdb=" O PHE G 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.688A pdb=" N ASN B 234 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.670A pdb=" N ASN C 234 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.648A pdb=" N ASN D 234 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.666A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.669A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.676A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) 959 hydrogen bonds defined for protein. 2814 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: 4.58 Time building geometry restraints manager: 5.67 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: 4340 1.34 - 1.46: 1988 1.46 - 1.57: 7335 1.57 - 1.69: 1 1.69 - 1.81: 84 Bond restraints: 13748 Sorted by residual: bond pdb=" CG LEU F 246 " pdb=" CD1 LEU F 246 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.39e+00 bond pdb=" CA VAL B 32 " pdb=" C VAL B 32 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.27e-02 6.20e+03 3.33e+00 bond pdb=" CG1 ILE A 170 " pdb=" CD1 ILE A 170 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.18e+00 bond pdb=" CB VAL E 239 " pdb=" CG1 VAL E 239 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 3.01e+00 bond pdb=" CG1 ILE E 170 " pdb=" CD1 ILE E 170 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.74e+00 ... (remaining 13743 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.85: 194 105.85 - 112.91: 7433 112.91 - 119.97: 4755 119.97 - 127.02: 6197 127.02 - 134.08: 62 Bond angle restraints: 18641 Sorted by residual: angle pdb=" N VAL B 65 " pdb=" CA VAL B 65 " pdb=" C VAL B 65 " ideal model delta sigma weight residual 113.43 106.39 7.04 1.09e+00 8.42e-01 4.17e+01 angle pdb=" C LYS E 278 " pdb=" N ARG E 279 " pdb=" CA ARG E 279 " ideal model delta sigma weight residual 120.82 129.61 -8.79 1.50e+00 4.44e-01 3.44e+01 angle pdb=" C ILE B 31 " pdb=" N VAL B 32 " pdb=" CA VAL B 32 " ideal model delta sigma weight residual 121.97 130.63 -8.66 1.80e+00 3.09e-01 2.31e+01 angle pdb=" C LYS E 60 " pdb=" N ILE E 61 " pdb=" CA ILE E 61 " ideal model delta sigma weight residual 121.97 130.29 -8.32 1.80e+00 3.09e-01 2.14e+01 angle pdb=" N VAL B 32 " pdb=" CA VAL B 32 " pdb=" C VAL B 32 " ideal model delta sigma weight residual 109.34 118.69 -9.35 2.08e+00 2.31e-01 2.02e+01 ... (remaining 18636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7371 18.00 - 36.00: 763 36.00 - 54.00: 115 54.00 - 72.00: 4 72.00 - 90.00: 7 Dihedral angle restraints: 8260 sinusoidal: 3171 harmonic: 5089 Sorted by residual: dihedral pdb=" CA ILE B 31 " pdb=" C ILE B 31 " pdb=" N VAL B 32 " pdb=" CA VAL B 32 " ideal model delta harmonic sigma weight residual -180.00 -127.72 -52.28 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA GLY F 90 " pdb=" C GLY F 90 " pdb=" N VAL F 91 " pdb=" CA VAL F 91 " ideal model delta harmonic sigma weight residual -180.00 -140.11 -39.89 0 5.00e+00 4.00e-02 6.36e+01 dihedral pdb=" CA LYS G 60 " pdb=" C LYS G 60 " pdb=" N ILE G 61 " pdb=" CA ILE G 61 " ideal model delta harmonic sigma weight residual -180.00 -146.56 -33.44 0 5.00e+00 4.00e-02 4.47e+01 ... (remaining 8257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1614 0.053 - 0.105: 491 0.105 - 0.158: 129 0.158 - 0.210: 36 0.210 - 0.263: 12 Chirality restraints: 2282 Sorted by residual: chirality pdb=" CB ILE B 31 " pdb=" CA ILE B 31 " pdb=" CG1 ILE B 31 " pdb=" CG2 ILE B 31 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL C 280 " pdb=" CA VAL C 280 " pdb=" CG1 VAL C 280 " pdb=" CG2 VAL C 280 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE A 233 " pdb=" CA ILE A 233 " pdb=" CG1 ILE A 233 " pdb=" CG2 ILE A 233 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2279 not shown) Planarity restraints: 2366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR F 270 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO F 271 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO F 271 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 271 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 270 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.81e+00 pdb=" N PRO A 271 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 270 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO D 271 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 271 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 271 " -0.033 5.00e-02 4.00e+02 ... (remaining 2363 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3947 2.81 - 3.34: 12389 3.34 - 3.86: 23192 3.86 - 4.38: 25817 4.38 - 4.90: 46424 Nonbonded interactions: 111769 Sorted by model distance: nonbonded pdb=" OH TYR F 194 " pdb=" O GLY F 229 " model vdw 2.294 2.440 nonbonded pdb=" O LYS D 202 " pdb=" OG1 THR D 206 " model vdw 2.303 2.440 nonbonded pdb=" OD1 ASP G 62 " pdb=" OG1 THR G 64 " model vdw 2.305 2.440 nonbonded pdb=" O LYS G 202 " pdb=" OG1 THR G 206 " model vdw 2.311 2.440 nonbonded pdb=" O LYS C 202 " pdb=" OG1 THR C 206 " model vdw 2.313 2.440 ... (remaining 111764 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.740 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 36.620 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 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 : 0.008 0.070 13748 Z= 0.509 Angle : 0.954 11.816 18641 Z= 0.536 Chirality : 0.058 0.263 2282 Planarity : 0.006 0.064 2366 Dihedral : 14.158 89.995 4984 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.97 % Favored : 95.98 % Rotamer: Outliers : 0.28 % Allowed : 9.57 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -3.97 (0.15), residues: 1764 helix: -2.49 (0.12), residues: 952 sheet: -2.71 (0.22), residues: 329 loop : -2.18 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 251 PHE 0.018 0.003 PHE C 277 TYR 0.010 0.002 TYR G 250 ARG 0.007 0.000 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 237 time to evaluate : 1.338 Fit side-chains REVERT: A 155 MET cc_start: 0.8792 (ptt) cc_final: 0.8507 (ptt) REVERT: B 47 MET cc_start: 0.6880 (ppp) cc_final: 0.6376 (ppp) REVERT: B 56 MET cc_start: 0.5808 (mtm) cc_final: 0.5227 (mmt) REVERT: B 155 MET cc_start: 0.8672 (ptt) cc_final: 0.8465 (ptt) REVERT: C 212 GLU cc_start: 0.8425 (tp30) cc_final: 0.8075 (tp30) REVERT: D 47 MET cc_start: 0.7268 (ppp) cc_final: 0.7012 (ppp) REVERT: D 61 ILE cc_start: 0.5018 (OUTLIER) cc_final: 0.4702 (pt) REVERT: D 155 MET cc_start: 0.8855 (ptt) cc_final: 0.8553 (ptm) REVERT: D 187 GLU cc_start: 0.8505 (tt0) cc_final: 0.8183 (tt0) REVERT: D 202 LYS cc_start: 0.8666 (mtmt) cc_final: 0.8460 (mtpp) REVERT: E 83 ILE cc_start: 0.8164 (pt) cc_final: 0.7948 (pt) REVERT: G 47 MET cc_start: 0.7164 (ppp) cc_final: 0.6933 (ppp) outliers start: 4 outliers final: 0 residues processed: 241 average time/residue: 0.3124 time to fit residues: 102.0603 Evaluate side-chains 164 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 50 ASN A 53 ASN A 167 ASN B 50 ASN B 53 ASN B 167 ASN C 30 ASN C 50 ASN C 167 ASN D 30 ASN D 167 ASN E 30 ASN E 167 ASN F 167 ASN G 50 ASN G 167 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13748 Z= 0.202 Angle : 0.531 7.430 18641 Z= 0.284 Chirality : 0.042 0.168 2282 Planarity : 0.004 0.040 2366 Dihedral : 5.427 42.981 1941 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 1.80 % Allowed : 12.62 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.90 (0.18), residues: 1764 helix: -0.38 (0.15), residues: 973 sheet: -1.96 (0.27), residues: 245 loop : -2.33 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 251 PHE 0.023 0.001 PHE B 277 TYR 0.005 0.001 TYR G 250 ARG 0.006 0.000 ARG G 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 202 time to evaluate : 1.482 Fit side-chains revert: symmetry clash REVERT: A 159 ASP cc_start: 0.8659 (p0) cc_final: 0.8261 (p0) REVERT: B 47 MET cc_start: 0.6955 (ppp) cc_final: 0.6520 (ppp) REVERT: B 56 MET cc_start: 0.6136 (mtm) cc_final: 0.5352 (mmt) REVERT: B 155 MET cc_start: 0.8694 (ptt) cc_final: 0.8494 (ptt) REVERT: C 212 GLU cc_start: 0.8337 (tp30) cc_final: 0.8100 (tp30) REVERT: D 47 MET cc_start: 0.7206 (ppp) cc_final: 0.6692 (ppp) REVERT: D 187 GLU cc_start: 0.8471 (tt0) cc_final: 0.8148 (tt0) REVERT: E 77 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7906 (mp) REVERT: E 123 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8549 (tt) REVERT: F 126 MET cc_start: 0.7925 (ptp) cc_final: 0.7417 (ptm) REVERT: G 123 LEU cc_start: 0.8844 (tp) cc_final: 0.8589 (mp) REVERT: G 161 LYS cc_start: 0.9012 (mtmt) cc_final: 0.8693 (mtmm) REVERT: G 239 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8354 (m) outliers start: 26 outliers final: 11 residues processed: 223 average time/residue: 0.2455 time to fit residues: 80.2161 Evaluate side-chains 185 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 239 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 127 optimal weight: 30.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.8066 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13748 Z= 0.313 Angle : 0.551 10.178 18641 Z= 0.292 Chirality : 0.043 0.145 2282 Planarity : 0.003 0.031 2366 Dihedral : 5.300 42.953 1939 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.82 % Favored : 95.12 % Rotamer: Outliers : 2.57 % Allowed : 14.63 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 1764 helix: 0.51 (0.16), residues: 966 sheet: -1.91 (0.25), residues: 329 loop : -1.80 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 251 PHE 0.026 0.002 PHE B 277 TYR 0.006 0.001 TYR D 250 ARG 0.005 0.000 ARG G 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 159 ASP cc_start: 0.8785 (p0) cc_final: 0.8463 (p0) REVERT: A 161 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8773 (mtmm) REVERT: B 155 MET cc_start: 0.8761 (ptt) cc_final: 0.8507 (ptt) REVERT: B 161 LYS cc_start: 0.9019 (mtmt) cc_final: 0.8813 (mtmm) REVERT: C 56 MET cc_start: 0.6020 (mtp) cc_final: 0.5633 (mmt) REVERT: C 212 GLU cc_start: 0.8420 (tp30) cc_final: 0.8194 (tp30) REVERT: D 47 MET cc_start: 0.7267 (ppp) cc_final: 0.6706 (ppp) REVERT: D 187 GLU cc_start: 0.8577 (tt0) cc_final: 0.8242 (tt0) REVERT: E 77 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7931 (mp) REVERT: E 123 LEU cc_start: 0.8798 (tt) cc_final: 0.8369 (tt) outliers start: 37 outliers final: 23 residues processed: 208 average time/residue: 0.2361 time to fit residues: 72.5258 Evaluate side-chains 197 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 213 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.8033 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13748 Z= 0.217 Angle : 0.502 7.072 18641 Z= 0.271 Chirality : 0.042 0.183 2282 Planarity : 0.003 0.027 2366 Dihedral : 5.006 38.860 1939 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 2.77 % Allowed : 16.16 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.19), residues: 1764 helix: 0.98 (0.16), residues: 973 sheet: -1.96 (0.25), residues: 315 loop : -1.85 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 251 PHE 0.023 0.001 PHE B 277 TYR 0.004 0.001 TYR D 250 ARG 0.003 0.000 ARG G 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 1.485 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8750 (mtmm) REVERT: B 56 MET cc_start: 0.6073 (mtm) cc_final: 0.5341 (mmt) REVERT: B 155 MET cc_start: 0.8706 (ptt) cc_final: 0.8484 (ptt) REVERT: B 255 GLU cc_start: 0.8130 (tt0) cc_final: 0.7865 (tt0) REVERT: C 56 MET cc_start: 0.5988 (mtp) cc_final: 0.5600 (mmt) REVERT: C 123 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8320 (mp) REVERT: C 155 MET cc_start: 0.8732 (ptp) cc_final: 0.8490 (ptm) REVERT: C 212 GLU cc_start: 0.8372 (tp30) cc_final: 0.8140 (tp30) REVERT: D 47 MET cc_start: 0.7286 (ppp) cc_final: 0.6732 (ppp) REVERT: D 187 GLU cc_start: 0.8487 (tt0) cc_final: 0.8130 (tt0) REVERT: E 77 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7861 (mp) REVERT: G 47 MET cc_start: 0.7028 (ppp) cc_final: 0.6647 (ppp) REVERT: G 155 MET cc_start: 0.8596 (ptp) cc_final: 0.8359 (ptm) outliers start: 40 outliers final: 21 residues processed: 205 average time/residue: 0.2335 time to fit residues: 71.9650 Evaluate side-chains 182 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 221 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 213 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.2980 chunk 151 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13748 Z= 0.182 Angle : 0.492 10.004 18641 Z= 0.263 Chirality : 0.042 0.242 2282 Planarity : 0.003 0.026 2366 Dihedral : 4.830 35.563 1939 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.65 % Favored : 95.29 % Rotamer: Outliers : 2.77 % Allowed : 18.10 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1764 helix: 1.33 (0.16), residues: 973 sheet: -1.80 (0.26), residues: 315 loop : -1.82 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 240 PHE 0.020 0.001 PHE C 277 TYR 0.004 0.001 TYR C 135 ARG 0.003 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 202 time to evaluate : 1.538 Fit side-chains revert: symmetry clash REVERT: B 47 MET cc_start: 0.6901 (ppp) cc_final: 0.6419 (ppp) REVERT: B 56 MET cc_start: 0.5807 (mtm) cc_final: 0.5231 (mmt) REVERT: B 155 MET cc_start: 0.8654 (ptt) cc_final: 0.8431 (ptt) REVERT: B 255 GLU cc_start: 0.8136 (tt0) cc_final: 0.7865 (tt0) REVERT: C 56 MET cc_start: 0.5831 (mtp) cc_final: 0.5422 (mmt) REVERT: C 123 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8310 (mp) REVERT: C 155 MET cc_start: 0.8753 (ptp) cc_final: 0.8493 (ptm) REVERT: C 212 GLU cc_start: 0.8346 (tp30) cc_final: 0.8095 (tp30) REVERT: D 47 MET cc_start: 0.7130 (ppp) cc_final: 0.6613 (ppp) REVERT: D 187 GLU cc_start: 0.8459 (tt0) cc_final: 0.8100 (tt0) REVERT: E 77 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7805 (mp) REVERT: E 239 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8406 (m) REVERT: G 47 MET cc_start: 0.7114 (ppp) cc_final: 0.6697 (ppp) REVERT: G 56 MET cc_start: 0.5586 (mtm) cc_final: 0.5265 (mmt) outliers start: 40 outliers final: 20 residues processed: 223 average time/residue: 0.2295 time to fit residues: 76.7166 Evaluate side-chains 199 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 227 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 140 optimal weight: 0.0370 chunk 78 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 overall best weight: 1.3862 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13748 Z= 0.242 Angle : 0.507 8.881 18641 Z= 0.272 Chirality : 0.042 0.243 2282 Planarity : 0.003 0.026 2366 Dihedral : 4.859 33.386 1939 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer: Outliers : 2.36 % Allowed : 19.90 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 1764 helix: 1.38 (0.16), residues: 973 sheet: -1.13 (0.29), residues: 245 loop : -2.29 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 251 PHE 0.019 0.001 PHE C 277 TYR 0.004 0.001 TYR G 250 ARG 0.003 0.000 ARG G 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6925 (ppp) REVERT: B 56 MET cc_start: 0.5871 (mtm) cc_final: 0.5271 (mmt) REVERT: B 155 MET cc_start: 0.8691 (ptt) cc_final: 0.8455 (ptt) REVERT: B 255 GLU cc_start: 0.8125 (tt0) cc_final: 0.7842 (tt0) REVERT: C 56 MET cc_start: 0.5932 (mtp) cc_final: 0.5343 (mmt) REVERT: C 123 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8331 (mp) REVERT: C 155 MET cc_start: 0.8748 (ptp) cc_final: 0.8485 (ptm) REVERT: C 212 GLU cc_start: 0.8372 (tp30) cc_final: 0.8131 (tp30) REVERT: D 47 MET cc_start: 0.7166 (ppp) cc_final: 0.6627 (ppp) REVERT: D 187 GLU cc_start: 0.8575 (tt0) cc_final: 0.8215 (tt0) REVERT: E 77 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7815 (mp) REVERT: E 239 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8445 (m) REVERT: G 47 MET cc_start: 0.7159 (ppp) cc_final: 0.6721 (ppp) REVERT: G 155 MET cc_start: 0.8673 (ptp) cc_final: 0.8425 (ptm) REVERT: G 239 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8395 (m) outliers start: 34 outliers final: 21 residues processed: 194 average time/residue: 0.2218 time to fit residues: 65.5422 Evaluate side-chains 197 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 171 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 239 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.1980 chunk 96 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 94 optimal weight: 0.0770 chunk 168 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13748 Z= 0.240 Angle : 0.504 9.825 18641 Z= 0.270 Chirality : 0.042 0.256 2282 Planarity : 0.003 0.024 2366 Dihedral : 4.836 31.646 1939 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.82 % Favored : 95.12 % Rotamer: Outliers : 2.43 % Allowed : 21.08 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1764 helix: 1.46 (0.16), residues: 973 sheet: -1.54 (0.27), residues: 315 loop : -1.94 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 251 PHE 0.018 0.001 PHE C 277 TYR 0.004 0.001 TYR G 250 ARG 0.002 0.000 ARG G 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 1.448 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6958 (ppp) REVERT: B 56 MET cc_start: 0.5824 (mtm) cc_final: 0.5281 (mmt) REVERT: B 155 MET cc_start: 0.8665 (ptt) cc_final: 0.8418 (ptt) REVERT: B 255 GLU cc_start: 0.8113 (tt0) cc_final: 0.7820 (tt0) REVERT: C 123 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8329 (mp) REVERT: C 155 MET cc_start: 0.8750 (ptp) cc_final: 0.8478 (ptm) REVERT: C 212 GLU cc_start: 0.8365 (tp30) cc_final: 0.8109 (tp30) REVERT: D 47 MET cc_start: 0.7178 (ppp) cc_final: 0.6642 (ppp) REVERT: D 187 GLU cc_start: 0.8569 (tt0) cc_final: 0.8205 (tt0) REVERT: E 77 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7806 (mp) REVERT: G 47 MET cc_start: 0.7126 (ppp) cc_final: 0.6709 (ppp) REVERT: G 56 MET cc_start: 0.5668 (mtp) cc_final: 0.5273 (mmt) REVERT: G 239 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8375 (m) outliers start: 35 outliers final: 23 residues processed: 200 average time/residue: 0.2150 time to fit residues: 65.8058 Evaluate side-chains 186 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 239 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 50 optimal weight: 0.0030 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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: 0.7988 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13748 Z= 0.156 Angle : 0.480 10.342 18641 Z= 0.257 Chirality : 0.042 0.250 2282 Planarity : 0.003 0.029 2366 Dihedral : 4.622 30.209 1939 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.97 % Favored : 95.98 % Rotamer: Outliers : 1.87 % Allowed : 21.84 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1764 helix: 1.76 (0.17), residues: 952 sheet: -1.49 (0.28), residues: 301 loop : -1.85 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 240 PHE 0.021 0.001 PHE D 277 TYR 0.004 0.000 TYR G 135 ARG 0.008 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 2.276 Fit side-chains revert: symmetry clash REVERT: B 56 MET cc_start: 0.5702 (mtm) cc_final: 0.5224 (mmt) REVERT: B 155 MET cc_start: 0.8550 (ptt) cc_final: 0.8320 (ptt) REVERT: B 255 GLU cc_start: 0.8096 (tt0) cc_final: 0.7814 (tt0) REVERT: C 56 MET cc_start: 0.5014 (mtm) cc_final: 0.4795 (mmt) REVERT: C 123 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8330 (mp) REVERT: C 155 MET cc_start: 0.8692 (ptp) cc_final: 0.8418 (ptm) REVERT: C 187 GLU cc_start: 0.8263 (tt0) cc_final: 0.7984 (tt0) REVERT: C 212 GLU cc_start: 0.8295 (tp30) cc_final: 0.8017 (tp30) REVERT: D 47 MET cc_start: 0.7158 (ppp) cc_final: 0.6645 (ppp) REVERT: E 77 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7834 (mp) REVERT: E 239 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8342 (m) REVERT: G 47 MET cc_start: 0.7351 (ppp) cc_final: 0.6938 (ppp) REVERT: G 56 MET cc_start: 0.5669 (mtp) cc_final: 0.5310 (mmt) REVERT: G 77 ILE cc_start: 0.8004 (mm) cc_final: 0.7682 (mp) REVERT: G 239 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8335 (m) outliers start: 27 outliers final: 16 residues processed: 194 average time/residue: 0.2146 time to fit residues: 65.4627 Evaluate side-chains 195 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 239 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7988 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13748 Z= 0.163 Angle : 0.489 10.325 18641 Z= 0.260 Chirality : 0.042 0.243 2282 Planarity : 0.003 0.024 2366 Dihedral : 4.583 30.865 1939 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.59 % Favored : 95.35 % Rotamer: Outliers : 2.15 % Allowed : 21.36 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.20), residues: 1764 helix: 1.83 (0.17), residues: 952 sheet: -1.30 (0.28), residues: 315 loop : -1.92 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 240 PHE 0.018 0.001 PHE C 277 TYR 0.003 0.001 TYR G 250 ARG 0.008 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 1.592 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7155 (ppp) cc_final: 0.6852 (ppp) REVERT: B 56 MET cc_start: 0.5717 (mtm) cc_final: 0.5241 (mmt) REVERT: B 155 MET cc_start: 0.8576 (ptt) cc_final: 0.8355 (ptt) REVERT: B 255 GLU cc_start: 0.8100 (tt0) cc_final: 0.7822 (tt0) REVERT: C 56 MET cc_start: 0.4823 (mtm) cc_final: 0.4611 (mmt) REVERT: C 123 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8345 (mp) REVERT: C 212 GLU cc_start: 0.8287 (tp30) cc_final: 0.8035 (tp30) REVERT: D 47 MET cc_start: 0.7141 (ppp) cc_final: 0.6624 (ppp) REVERT: E 77 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7832 (mp) REVERT: E 83 ILE cc_start: 0.7869 (pt) cc_final: 0.7624 (pt) REVERT: E 239 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8392 (m) REVERT: G 47 MET cc_start: 0.7350 (ppp) cc_final: 0.6946 (ppp) REVERT: G 56 MET cc_start: 0.5632 (mtp) cc_final: 0.5337 (mmt) REVERT: G 239 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8369 (m) outliers start: 31 outliers final: 21 residues processed: 197 average time/residue: 0.1998 time to fit residues: 62.2946 Evaluate side-chains 201 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 239 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13748 Z= 0.206 Angle : 0.513 10.782 18641 Z= 0.270 Chirality : 0.042 0.236 2282 Planarity : 0.003 0.024 2366 Dihedral : 4.642 30.889 1939 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.07 % Rotamer: Outliers : 1.80 % Allowed : 21.91 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.20), residues: 1764 helix: 1.78 (0.17), residues: 952 sheet: -0.88 (0.30), residues: 245 loop : -2.21 (0.22), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 251 PHE 0.026 0.001 PHE D 277 TYR 0.004 0.001 TYR G 250 ARG 0.008 0.000 ARG B 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7166 (ppp) cc_final: 0.6845 (ppp) REVERT: B 56 MET cc_start: 0.5847 (mtm) cc_final: 0.5321 (mmt) REVERT: B 155 MET cc_start: 0.8630 (ptt) cc_final: 0.8397 (ptt) REVERT: B 255 GLU cc_start: 0.8113 (tt0) cc_final: 0.7825 (tt0) REVERT: C 123 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8336 (mp) REVERT: C 155 MET cc_start: 0.8798 (ptp) cc_final: 0.8519 (ptm) REVERT: C 212 GLU cc_start: 0.8333 (tp30) cc_final: 0.8063 (tp30) REVERT: D 47 MET cc_start: 0.7156 (ppp) cc_final: 0.6647 (ppp) REVERT: D 56 MET cc_start: 0.5779 (ppp) cc_final: 0.5392 (ppp) REVERT: E 77 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7760 (mp) REVERT: E 239 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8422 (m) REVERT: F 270 TYR cc_start: 0.8979 (m-80) cc_final: 0.8498 (m-80) REVERT: G 47 MET cc_start: 0.7368 (ppp) cc_final: 0.6959 (ppp) REVERT: G 56 MET cc_start: 0.5624 (mtp) cc_final: 0.5423 (mmt) REVERT: G 239 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8390 (m) outliers start: 26 outliers final: 21 residues processed: 186 average time/residue: 0.1983 time to fit residues: 58.7704 Evaluate side-chains 193 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 239 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 139 optimal weight: 0.0270 chunk 58 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.0050 chunk 122 optimal weight: 0.9990 overall best weight: 0.4652 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.132404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.096274 restraints weight = 16994.756| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.89 r_work: 0.2866 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13748 Z= 0.137 Angle : 0.503 17.671 18641 Z= 0.261 Chirality : 0.042 0.236 2282 Planarity : 0.003 0.025 2366 Dihedral : 4.477 30.048 1939 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 1.66 % Allowed : 22.19 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1764 helix: 1.96 (0.17), residues: 952 sheet: -1.31 (0.28), residues: 301 loop : -1.79 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 240 PHE 0.016 0.001 PHE C 277 TYR 0.007 0.000 TYR F 135 ARG 0.008 0.000 ARG B 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2656.15 seconds wall clock time: 48 minutes 40.50 seconds (2920.50 seconds total)