Starting phenix.real_space_refine on Thu Feb 15 23:18:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyl_21463/02_2024/6vyl_21463.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyl_21463/02_2024/6vyl_21463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyl_21463/02_2024/6vyl_21463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyl_21463/02_2024/6vyl_21463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyl_21463/02_2024/6vyl_21463.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyl_21463/02_2024/6vyl_21463.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 8778 2.51 5 N 2387 2.21 5 O 2464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 46": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E GLU 181": "OE1" <-> "OE2" Residue "F ARG 46": "NH1" <-> "NH2" Residue "F GLU 181": "OE1" <-> "OE2" Residue "G ARG 46": "NH1" <-> "NH2" Residue "G GLU 181": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13671 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1953 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 5, 'TRANS': 250} Chain: "B" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1953 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 5, 'TRANS': 250} Chain: "C" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1953 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 5, 'TRANS': 250} Chain: "D" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1953 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 5, 'TRANS': 250} Chain: "E" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1953 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 5, 'TRANS': 250} Chain: "F" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1953 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 5, 'TRANS': 250} Chain: "G" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1953 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 5, 'TRANS': 250} Time building chain proxies: 7.46, per 1000 atoms: 0.55 Number of scatterers: 13671 At special positions: 0 Unit cell: (98.8, 98.8, 123.5, 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 2464 8.00 N 2387 7.00 C 8778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.85 Conformation dependent library (CDL) restraints added in 2.4 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 22 sheets defined 51.2% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 27 through 60 removed outlier: 3.604A pdb=" N ILE A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 60 " --> pdb=" O MET A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 87 removed outlier: 3.727A pdb=" N ALA A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 111 removed outlier: 3.628A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.623A pdb=" N LEU A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.560A pdb=" N THR A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 263 removed outlier: 3.607A pdb=" N GLU A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 60 removed outlier: 3.604A pdb=" N ILE B 31 " --> pdb=" O TYR B 27 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 60 " --> pdb=" O MET B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 removed outlier: 3.726A pdb=" N ALA B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 111 removed outlier: 3.628A pdb=" N ALA B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 127 removed outlier: 3.622A pdb=" N LEU B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.559A pdb=" N THR B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 263 removed outlier: 3.607A pdb=" N GLU B 255 " --> pdb=" O TRP B 251 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 60 removed outlier: 3.604A pdb=" N ILE C 31 " --> pdb=" O TYR C 27 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA C 33 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 87 removed outlier: 3.727A pdb=" N ALA C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 111 removed outlier: 3.627A pdb=" N ALA C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.622A pdb=" N LEU C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.559A pdb=" N THR C 206 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER C 211 " --> pdb=" O ASN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 263 removed outlier: 3.607A pdb=" N GLU C 255 " --> pdb=" O TRP C 251 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 60 removed outlier: 3.603A pdb=" N ILE D 31 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA D 33 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS D 60 " --> pdb=" O MET D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 87 removed outlier: 3.727A pdb=" N ALA D 79 " --> pdb=" O TYR D 75 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 111 removed outlier: 3.628A pdb=" N ALA D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.622A pdb=" N LEU D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.559A pdb=" N THR D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER D 211 " --> pdb=" O ASN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 263 removed outlier: 3.606A pdb=" N GLU D 255 " --> pdb=" O TRP D 251 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 60 removed outlier: 3.605A pdb=" N ILE E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA E 33 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS E 60 " --> pdb=" O MET E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 87 removed outlier: 3.726A pdb=" N ALA E 79 " --> pdb=" O TYR E 75 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 87 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 111 removed outlier: 3.628A pdb=" N ALA E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 127 removed outlier: 3.622A pdb=" N LEU E 123 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 197 through 212 removed outlier: 3.558A pdb=" N THR E 206 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 209 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER E 211 " --> pdb=" O ASN E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 263 removed outlier: 3.607A pdb=" N GLU E 255 " --> pdb=" O TRP E 251 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG E 256 " --> pdb=" O ASP E 252 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 60 removed outlier: 3.604A pdb=" N ILE F 31 " --> pdb=" O TYR F 27 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA F 33 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE F 57 " --> pdb=" O ASN F 53 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS F 60 " --> pdb=" O MET F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 87 removed outlier: 3.727A pdb=" N ALA F 79 " --> pdb=" O TYR F 75 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY F 87 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 111 removed outlier: 3.627A pdb=" N ALA F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 127 removed outlier: 3.623A pdb=" N LEU F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL F 125 " --> pdb=" O GLY F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 197 through 212 removed outlier: 3.559A pdb=" N THR F 206 " --> pdb=" O LYS F 202 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE F 209 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER F 211 " --> pdb=" O ASN F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 263 removed outlier: 3.606A pdb=" N GLU F 255 " --> pdb=" O TRP F 251 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP F 262 " --> pdb=" O LYS F 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 60 removed outlier: 3.604A pdb=" N ILE G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA G 33 " --> pdb=" O VAL G 29 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE G 57 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER G 58 " --> pdb=" O ARG G 54 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS G 60 " --> pdb=" O MET G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 87 removed outlier: 3.726A pdb=" N ALA G 79 " --> pdb=" O TYR G 75 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY G 87 " --> pdb=" O ILE G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 111 removed outlier: 3.627A pdb=" N ALA G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 127 removed outlier: 3.622A pdb=" N LEU G 123 " --> pdb=" O ALA G 119 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL G 125 " --> pdb=" O GLY G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 171 Processing helix chain 'G' and resid 197 through 212 removed outlier: 3.559A pdb=" N THR G 206 " --> pdb=" O LYS G 202 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE G 209 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER G 211 " --> pdb=" O ASN G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 263 removed outlier: 3.607A pdb=" N GLU G 255 " --> pdb=" O TRP G 251 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG G 256 " --> pdb=" O ASP G 252 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 137 removed outlier: 6.934A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 162 " --> pdb=" O ASN G 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.562A pdb=" N ILE B 162 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 185 Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 192 removed outlier: 6.044A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 278 through 279 removed outlier: 3.618A pdb=" N MET G 273 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N MET A 273 " --> pdb=" O ASN G 276 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N MET B 273 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP A 274 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N MET C 273 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP B 274 " --> pdb=" O MET C 273 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL C 275 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N MET D 273 " --> pdb=" O GLN C 272 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP C 274 " --> pdb=" O MET D 273 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL D 275 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N MET E 273 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP D 274 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL E 275 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N MET F 273 " --> pdb=" O GLN E 272 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASP E 274 " --> pdb=" O MET F 273 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL F 275 " --> pdb=" O ASP E 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.554A pdb=" N ILE C 162 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 185 Processing sheet with id=AA8, first strand: chain 'B' and resid 188 through 192 removed outlier: 6.044A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.621A pdb=" N ILE D 162 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 183 through 185 Processing sheet with id=AB2, first strand: chain 'C' and resid 188 through 192 removed outlier: 6.044A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 175 through 177 removed outlier: 3.556A pdb=" N ILE E 162 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 183 through 185 Processing sheet with id=AB5, first strand: chain 'D' and resid 188 through 192 removed outlier: 6.044A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 175 through 177 removed outlier: 3.511A pdb=" N ILE F 162 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 183 through 185 Processing sheet with id=AB8, first strand: chain 'E' and resid 188 through 192 removed outlier: 6.044A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 175 through 177 removed outlier: 3.574A pdb=" N ILE G 162 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 183 through 185 Processing sheet with id=AC2, first strand: chain 'F' and resid 188 through 192 removed outlier: 6.043A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 183 through 185 Processing sheet with id=AC4, first strand: chain 'G' and resid 188 through 192 removed outlier: 6.044A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) 769 hydrogen bonds defined for protein. 2241 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: 4.32 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3947 1.33 - 1.45: 1929 1.45 - 1.57: 7886 1.57 - 1.69: 0 1.69 - 1.80: 84 Bond restraints: 13846 Sorted by residual: bond pdb=" CB ILE A 233 " pdb=" CG2 ILE A 233 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.07e+00 bond pdb=" CB ILE F 233 " pdb=" CG2 ILE F 233 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.07e+00 bond pdb=" CB ILE E 233 " pdb=" CG2 ILE E 233 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.05e+00 bond pdb=" CB ILE G 233 " pdb=" CG2 ILE G 233 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.05e+00 bond pdb=" CB ILE B 233 " pdb=" CG2 ILE B 233 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.04e+00 ... (remaining 13841 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.10: 187 106.10 - 113.06: 7663 113.06 - 120.02: 5041 120.02 - 126.98: 5824 126.98 - 133.94: 59 Bond angle restraints: 18774 Sorted by residual: angle pdb=" N VAL D 125 " pdb=" CA VAL D 125 " pdb=" C VAL D 125 " ideal model delta sigma weight residual 112.96 108.66 4.30 1.00e+00 1.00e+00 1.85e+01 angle pdb=" N VAL G 125 " pdb=" CA VAL G 125 " pdb=" C VAL G 125 " ideal model delta sigma weight residual 112.96 108.68 4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" N VAL A 125 " pdb=" CA VAL A 125 " pdb=" C VAL A 125 " ideal model delta sigma weight residual 112.96 108.69 4.27 1.00e+00 1.00e+00 1.82e+01 angle pdb=" N VAL F 125 " pdb=" CA VAL F 125 " pdb=" C VAL F 125 " ideal model delta sigma weight residual 112.96 108.69 4.27 1.00e+00 1.00e+00 1.82e+01 angle pdb=" N VAL B 125 " pdb=" CA VAL B 125 " pdb=" C VAL B 125 " ideal model delta sigma weight residual 112.96 108.70 4.26 1.00e+00 1.00e+00 1.81e+01 ... (remaining 18769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 7286 15.51 - 31.02: 785 31.02 - 46.54: 210 46.54 - 62.05: 21 62.05 - 77.56: 21 Dihedral angle restraints: 8323 sinusoidal: 3192 harmonic: 5131 Sorted by residual: dihedral pdb=" CA LYS D 60 " pdb=" C LYS D 60 " pdb=" N ILE D 61 " pdb=" CA ILE D 61 " ideal model delta harmonic sigma weight residual 180.00 -146.04 -33.96 0 5.00e+00 4.00e-02 4.61e+01 dihedral pdb=" CA LYS F 60 " pdb=" C LYS F 60 " pdb=" N ILE F 61 " pdb=" CA ILE F 61 " ideal model delta harmonic sigma weight residual 180.00 -146.08 -33.92 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA LYS B 60 " pdb=" C LYS B 60 " pdb=" N ILE B 61 " pdb=" CA ILE B 61 " ideal model delta harmonic sigma weight residual -180.00 -146.08 -33.92 0 5.00e+00 4.00e-02 4.60e+01 ... (remaining 8320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1182 0.036 - 0.072: 678 0.072 - 0.107: 309 0.107 - 0.143: 104 0.143 - 0.179: 30 Chirality restraints: 2303 Sorted by residual: chirality pdb=" CA PRO E 182 " pdb=" N PRO E 182 " pdb=" C PRO E 182 " pdb=" CB PRO E 182 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CA PRO C 182 " pdb=" N PRO C 182 " pdb=" C PRO C 182 " pdb=" CB PRO C 182 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA PRO F 182 " pdb=" N PRO F 182 " pdb=" C PRO F 182 " pdb=" CB PRO F 182 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 2300 not shown) Planarity restraints: 2380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 270 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.75e+00 pdb=" N PRO E 271 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO E 271 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 271 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 270 " 0.046 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PRO F 271 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO F 271 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 271 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 270 " 0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO G 271 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 271 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 271 " 0.039 5.00e-02 4.00e+02 ... (remaining 2377 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3945 2.81 - 3.34: 12075 3.34 - 3.86: 21799 3.86 - 4.38: 25160 4.38 - 4.90: 44354 Nonbonded interactions: 107333 Sorted by model distance: nonbonded pdb=" OD1 ASP F 199 " pdb=" NH2 ARG G 259 " model vdw 2.293 2.520 nonbonded pdb=" OD1 ASP D 199 " pdb=" NH2 ARG E 259 " model vdw 2.305 2.520 nonbonded pdb=" OE2 GLU F 220 " pdb=" OG1 THR F 222 " model vdw 2.306 2.440 nonbonded pdb=" OE2 GLU G 220 " pdb=" OG1 THR G 222 " model vdw 2.306 2.440 nonbonded pdb=" OE2 GLU D 220 " pdb=" OG1 THR D 222 " model vdw 2.306 2.440 ... (remaining 107328 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: 0.330 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: 1.830 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 37.990 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 0.060 13846 Z= 0.548 Angle : 0.847 6.612 18774 Z= 0.489 Chirality : 0.055 0.179 2303 Planarity : 0.007 0.070 2380 Dihedral : 14.419 77.561 5019 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.48 % Allowed : 8.72 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -4.60 (0.15), residues: 1778 helix: -3.39 (0.10), residues: 903 sheet: -2.05 (0.26), residues: 294 loop : -2.53 (0.22), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 251 PHE 0.013 0.003 PHE D 178 TYR 0.009 0.002 TYR D 250 ARG 0.008 0.001 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 302 time to evaluate : 1.620 Fit side-chains REVERT: A 74 ARG cc_start: 0.7124 (ttt180) cc_final: 0.6908 (ttp80) REVERT: A 245 ASP cc_start: 0.8238 (p0) cc_final: 0.8037 (p0) REVERT: B 80 PHE cc_start: 0.8408 (m-80) cc_final: 0.7792 (m-80) REVERT: B 149 GLN cc_start: 0.8207 (mp10) cc_final: 0.7541 (mp10) REVERT: B 202 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8287 (ttmt) REVERT: C 134 GLU cc_start: 0.7268 (tt0) cc_final: 0.6742 (tt0) REVERT: C 245 ASP cc_start: 0.8166 (p0) cc_final: 0.7905 (p0) REVERT: D 74 ARG cc_start: 0.7329 (ttt180) cc_final: 0.6928 (ttp80) REVERT: D 80 PHE cc_start: 0.8455 (m-80) cc_final: 0.8214 (m-80) REVERT: D 207 ASN cc_start: 0.7819 (m-40) cc_final: 0.7337 (m-40) REVERT: D 272 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8505 (mm-40) REVERT: E 179 SER cc_start: 0.7805 (t) cc_final: 0.7587 (t) REVERT: F 56 MET cc_start: 0.7148 (mmt) cc_final: 0.6733 (mmp) REVERT: F 74 ARG cc_start: 0.7004 (ttt180) cc_final: 0.6795 (ttp80) REVERT: F 150 ILE cc_start: 0.9172 (mp) cc_final: 0.8884 (mp) REVERT: G 134 GLU cc_start: 0.7268 (tt0) cc_final: 0.6896 (tt0) REVERT: G 276 ASN cc_start: 0.8413 (m-40) cc_final: 0.8064 (m110) outliers start: 7 outliers final: 3 residues processed: 309 average time/residue: 0.2637 time to fit residues: 116.3586 Evaluate side-chains 229 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 226 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain E residue 225 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 149 GLN A 210 GLN B 112 GLN B 149 GLN C 112 GLN C 149 GLN D 112 GLN D 149 GLN E 112 GLN E 149 GLN F 112 GLN F 149 GLN F 210 GLN G 112 GLN G 149 GLN G 210 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13846 Z= 0.156 Angle : 0.490 5.521 18774 Z= 0.271 Chirality : 0.042 0.143 2303 Planarity : 0.004 0.059 2380 Dihedral : 5.693 33.934 1959 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.30 % Allowed : 13.80 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -2.83 (0.18), residues: 1778 helix: -1.70 (0.15), residues: 917 sheet: -1.64 (0.26), residues: 308 loop : -1.88 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 251 PHE 0.010 0.001 PHE A 235 TYR 0.011 0.001 TYR F 250 ARG 0.005 0.000 ARG C 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 218 time to evaluate : 1.551 Fit side-chains REVERT: A 245 ASP cc_start: 0.8025 (p0) cc_final: 0.7671 (p0) REVERT: A 272 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8576 (mm-40) REVERT: B 105 LEU cc_start: 0.6422 (mt) cc_final: 0.6116 (mp) REVERT: B 126 MET cc_start: 0.7593 (mtt) cc_final: 0.7335 (mtt) REVERT: B 272 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8254 (mm-40) REVERT: C 134 GLU cc_start: 0.7286 (tt0) cc_final: 0.6659 (tt0) REVERT: C 272 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8218 (mm-40) REVERT: C 274 ASP cc_start: 0.8074 (t0) cc_final: 0.7697 (t0) REVERT: D 74 ARG cc_start: 0.7136 (ttt180) cc_final: 0.6767 (ttp80) REVERT: D 80 PHE cc_start: 0.8311 (m-80) cc_final: 0.7981 (m-80) REVERT: D 115 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8623 (mp) REVERT: D 207 ASN cc_start: 0.7957 (m-40) cc_final: 0.7507 (m-40) REVERT: D 210 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8272 (mm110) REVERT: D 221 MET cc_start: 0.7242 (mtp) cc_final: 0.7001 (mtp) REVERT: D 272 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8469 (mm-40) REVERT: F 56 MET cc_start: 0.7093 (mmt) cc_final: 0.6661 (mmp) REVERT: F 115 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8620 (mp) outliers start: 19 outliers final: 10 residues processed: 229 average time/residue: 0.2733 time to fit residues: 90.4753 Evaluate side-chains 217 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 205 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 222 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 141 optimal weight: 0.1980 chunk 157 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 GLN E 149 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13846 Z= 0.205 Angle : 0.474 6.095 18774 Z= 0.260 Chirality : 0.042 0.141 2303 Planarity : 0.004 0.052 2380 Dihedral : 5.403 37.276 1957 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.99 % Allowed : 15.73 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -1.76 (0.19), residues: 1778 helix: -0.79 (0.17), residues: 910 sheet: -0.78 (0.26), residues: 308 loop : -1.75 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 240 PHE 0.007 0.001 PHE F 235 TYR 0.012 0.001 TYR A 250 ARG 0.006 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 210 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7403 (mp-120) REVERT: A 210 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8335 (mm110) REVERT: A 272 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8498 (mm-40) REVERT: B 149 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7060 (mp-120) REVERT: B 272 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8411 (mm-40) REVERT: C 134 GLU cc_start: 0.7358 (tt0) cc_final: 0.6706 (tt0) REVERT: D 74 ARG cc_start: 0.7188 (ttt180) cc_final: 0.6807 (ttp80) REVERT: D 115 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8601 (mp) REVERT: D 207 ASN cc_start: 0.7956 (m-40) cc_final: 0.7516 (m-40) REVERT: D 272 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8325 (mm-40) REVERT: E 74 ARG cc_start: 0.6776 (ttt180) cc_final: 0.6478 (ttp80) REVERT: E 210 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8304 (mm110) REVERT: F 56 MET cc_start: 0.7129 (mmt) cc_final: 0.6611 (mmp) outliers start: 29 outliers final: 14 residues processed: 228 average time/residue: 0.2565 time to fit residues: 84.9556 Evaluate side-chains 216 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 222 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 169 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 GLN F 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13846 Z= 0.313 Angle : 0.516 7.675 18774 Z= 0.278 Chirality : 0.044 0.145 2303 Planarity : 0.004 0.055 2380 Dihedral : 5.532 53.530 1957 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.47 % Allowed : 17.24 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -1.41 (0.20), residues: 1778 helix: -0.49 (0.17), residues: 924 sheet: -0.77 (0.27), residues: 308 loop : -1.52 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 240 PHE 0.009 0.001 PHE G 268 TYR 0.014 0.001 TYR A 250 ARG 0.004 0.000 ARG D 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 1.436 Fit side-chains REVERT: A 149 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7500 (mp-120) REVERT: A 245 ASP cc_start: 0.8244 (p0) cc_final: 0.7824 (p0) REVERT: B 126 MET cc_start: 0.7624 (mtt) cc_final: 0.7404 (mtt) REVERT: B 149 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7016 (mp-120) REVERT: B 272 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8406 (mm-40) REVERT: C 80 PHE cc_start: 0.8455 (m-80) cc_final: 0.8010 (m-80) REVERT: C 134 GLU cc_start: 0.7406 (tt0) cc_final: 0.6710 (tt0) REVERT: C 149 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7787 (mp-120) REVERT: D 74 ARG cc_start: 0.7200 (ttt180) cc_final: 0.6846 (ttp80) REVERT: D 80 PHE cc_start: 0.8339 (m-80) cc_final: 0.8098 (m-80) REVERT: D 115 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8692 (mp) REVERT: D 149 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7749 (mm110) REVERT: D 207 ASN cc_start: 0.8051 (m-40) cc_final: 0.7630 (m-40) REVERT: E 74 ARG cc_start: 0.6762 (ttt180) cc_final: 0.6531 (ttp80) REVERT: E 210 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8093 (mm110) REVERT: F 56 MET cc_start: 0.7036 (mmt) cc_final: 0.6393 (mmp) REVERT: F 134 GLU cc_start: 0.7404 (tt0) cc_final: 0.7046 (tt0) REVERT: G 46 ARG cc_start: 0.7509 (mmm-85) cc_final: 0.6923 (mmt90) outliers start: 36 outliers final: 24 residues processed: 241 average time/residue: 0.2470 time to fit residues: 86.6639 Evaluate side-chains 245 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 222 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 144 optimal weight: 0.0370 chunk 116 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 86 optimal weight: 0.5980 chunk 151 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN D 149 GLN F 149 GLN ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13846 Z= 0.167 Angle : 0.453 5.069 18774 Z= 0.250 Chirality : 0.041 0.138 2303 Planarity : 0.003 0.054 2380 Dihedral : 5.153 51.989 1955 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.58 % Allowed : 18.75 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -1.08 (0.20), residues: 1778 helix: -0.19 (0.17), residues: 924 sheet: -0.68 (0.27), residues: 308 loop : -1.39 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 240 PHE 0.009 0.001 PHE E 235 TYR 0.012 0.001 TYR A 250 ARG 0.004 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 211 time to evaluate : 1.566 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7439 (mp-120) REVERT: A 245 ASP cc_start: 0.8237 (p0) cc_final: 0.7856 (p0) REVERT: B 126 MET cc_start: 0.7599 (mtt) cc_final: 0.7356 (mtt) REVERT: B 149 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.6943 (mp-120) REVERT: B 272 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8475 (mm-40) REVERT: C 46 ARG cc_start: 0.7416 (mmm-85) cc_final: 0.7176 (tpp80) REVERT: C 134 GLU cc_start: 0.7303 (tt0) cc_final: 0.6624 (tt0) REVERT: D 74 ARG cc_start: 0.7158 (ttt180) cc_final: 0.6826 (ttp80) REVERT: D 115 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8633 (mp) REVERT: D 207 ASN cc_start: 0.8023 (m-40) cc_final: 0.7613 (m-40) REVERT: E 74 ARG cc_start: 0.6794 (ttt180) cc_final: 0.6560 (ttp80) REVERT: F 56 MET cc_start: 0.7015 (mmt) cc_final: 0.6396 (mmp) REVERT: F 277 PHE cc_start: 0.7443 (m-10) cc_final: 0.7188 (m-10) REVERT: G 46 ARG cc_start: 0.7526 (mmm-85) cc_final: 0.6908 (mmt90) outliers start: 23 outliers final: 14 residues processed: 220 average time/residue: 0.2709 time to fit residues: 85.4778 Evaluate side-chains 226 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 209 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 115 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 169 optimal weight: 0.0370 chunk 140 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN C 149 GLN D 149 GLN F 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13846 Z= 0.132 Angle : 0.440 8.093 18774 Z= 0.239 Chirality : 0.041 0.137 2303 Planarity : 0.003 0.055 2380 Dihedral : 4.956 57.146 1955 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.99 % Allowed : 18.96 % Favored : 79.05 % 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: -0.70 (0.20), residues: 1778 helix: 0.14 (0.17), residues: 924 sheet: -0.49 (0.27), residues: 308 loop : -1.27 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 240 PHE 0.009 0.001 PHE E 235 TYR 0.012 0.001 TYR A 250 ARG 0.011 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 1.696 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7406 (mp-120) REVERT: A 245 ASP cc_start: 0.8196 (p0) cc_final: 0.7849 (p0) REVERT: A 272 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8598 (mm-40) REVERT: B 149 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.6966 (mp-120) REVERT: C 272 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8259 (mm-40) REVERT: D 74 ARG cc_start: 0.7058 (ttt180) cc_final: 0.6824 (ttp80) REVERT: D 115 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8581 (mp) REVERT: D 207 ASN cc_start: 0.7956 (m-40) cc_final: 0.7553 (m-40) REVERT: E 74 ARG cc_start: 0.6852 (ttt180) cc_final: 0.6484 (ttp-170) REVERT: F 56 MET cc_start: 0.7009 (mmt) cc_final: 0.6494 (mmp) REVERT: F 277 PHE cc_start: 0.7376 (m-10) cc_final: 0.7144 (m-10) outliers start: 29 outliers final: 16 residues processed: 225 average time/residue: 0.2576 time to fit residues: 84.6824 Evaluate side-chains 222 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 222 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.0980 chunk 96 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN C 149 GLN D 149 GLN E 149 GLN F 149 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13846 Z= 0.130 Angle : 0.428 4.842 18774 Z= 0.235 Chirality : 0.041 0.134 2303 Planarity : 0.003 0.055 2380 Dihedral : 4.838 54.521 1955 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.99 % Allowed : 19.02 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1778 helix: 0.33 (0.17), residues: 924 sheet: -0.37 (0.27), residues: 308 loop : -1.20 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 240 PHE 0.009 0.001 PHE E 235 TYR 0.012 0.001 TYR A 250 ARG 0.003 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 203 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7401 (mp-120) REVERT: A 245 ASP cc_start: 0.8209 (p0) cc_final: 0.7857 (p0) REVERT: A 272 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8560 (mm-40) REVERT: B 149 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.6989 (mp-120) REVERT: C 272 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8252 (mm-40) REVERT: D 115 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8577 (mp) REVERT: D 207 ASN cc_start: 0.7886 (m-40) cc_final: 0.7461 (m-40) REVERT: D 272 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8258 (mm-40) REVERT: E 74 ARG cc_start: 0.6829 (ttt180) cc_final: 0.6516 (ttp-170) REVERT: F 56 MET cc_start: 0.6853 (mmt) cc_final: 0.6408 (mmp) outliers start: 29 outliers final: 19 residues processed: 221 average time/residue: 0.2596 time to fit residues: 82.9584 Evaluate side-chains 219 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 197 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 141 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN C 149 GLN D 149 GLN E 149 GLN F 149 GLN F 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.002 0.028 13846 Z= 0.134 Angle : 0.441 8.933 18774 Z= 0.238 Chirality : 0.041 0.135 2303 Planarity : 0.003 0.054 2380 Dihedral : 4.683 41.044 1955 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.85 % Allowed : 19.44 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1778 helix: 0.51 (0.17), residues: 924 sheet: -0.29 (0.27), residues: 308 loop : -1.15 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 240 PHE 0.016 0.001 PHE F 277 TYR 0.013 0.000 TYR A 250 ARG 0.005 0.000 ARG D 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 199 time to evaluate : 1.505 Fit side-chains REVERT: A 149 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7404 (mp-120) REVERT: A 272 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8553 (mm-40) REVERT: B 149 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7001 (mp-120) REVERT: C 272 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8288 (mm-40) REVERT: D 115 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8557 (mp) REVERT: D 207 ASN cc_start: 0.7813 (m-40) cc_final: 0.7408 (m-40) REVERT: D 272 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8608 (mm110) REVERT: E 74 ARG cc_start: 0.6818 (ttt180) cc_final: 0.6514 (ttp-170) REVERT: E 276 ASN cc_start: 0.8006 (m-40) cc_final: 0.7541 (m110) REVERT: F 56 MET cc_start: 0.6751 (mmt) cc_final: 0.6400 (mmp) outliers start: 27 outliers final: 23 residues processed: 214 average time/residue: 0.2585 time to fit residues: 80.6715 Evaluate side-chains 219 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 222 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.0470 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 156 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13846 Z= 0.128 Angle : 0.437 7.520 18774 Z= 0.237 Chirality : 0.041 0.134 2303 Planarity : 0.003 0.055 2380 Dihedral : 4.501 28.632 1953 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.58 % Allowed : 19.23 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1778 helix: 0.70 (0.17), residues: 924 sheet: -0.24 (0.28), residues: 294 loop : -1.10 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 251 PHE 0.013 0.001 PHE F 277 TYR 0.013 0.001 TYR A 250 ARG 0.005 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 195 time to evaluate : 1.657 Fit side-chains REVERT: A 149 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7402 (mp-120) REVERT: A 272 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8540 (mm-40) REVERT: B 126 MET cc_start: 0.7564 (mtt) cc_final: 0.7332 (mtt) REVERT: B 149 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7016 (mp-120) REVERT: C 134 GLU cc_start: 0.7275 (tt0) cc_final: 0.7012 (tt0) REVERT: C 260 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8192 (mt-10) REVERT: C 272 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8328 (mm-40) REVERT: D 115 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8535 (mp) REVERT: D 207 ASN cc_start: 0.7779 (m-40) cc_final: 0.7362 (m-40) REVERT: E 74 ARG cc_start: 0.6788 (ttt180) cc_final: 0.6494 (ttp-170) REVERT: F 56 MET cc_start: 0.6786 (mmt) cc_final: 0.6403 (mmp) REVERT: F 272 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8415 (mm110) REVERT: G 221 MET cc_start: 0.7293 (mtp) cc_final: 0.7032 (mtp) outliers start: 23 outliers final: 19 residues processed: 209 average time/residue: 0.2708 time to fit residues: 82.4895 Evaluate side-chains 211 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 189 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 174 optimal weight: 0.0870 chunk 160 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 0.3980 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13846 Z= 0.163 Angle : 0.450 6.926 18774 Z= 0.243 Chirality : 0.041 0.160 2303 Planarity : 0.003 0.054 2380 Dihedral : 4.536 28.536 1953 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.65 % Allowed : 19.85 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.20), residues: 1778 helix: 0.79 (0.17), residues: 924 sheet: -0.23 (0.27), residues: 308 loop : -1.08 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 240 PHE 0.008 0.001 PHE F 277 TYR 0.013 0.001 TYR A 250 ARG 0.007 0.000 ARG D 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 1.642 Fit side-chains REVERT: A 149 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7431 (mp-120) REVERT: A 212 GLU cc_start: 0.8691 (tp30) cc_final: 0.8448 (tp30) REVERT: A 272 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8453 (mm-40) REVERT: B 126 MET cc_start: 0.7555 (mtt) cc_final: 0.7318 (mtt) REVERT: B 149 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.6974 (mp-120) REVERT: C 134 GLU cc_start: 0.7314 (tt0) cc_final: 0.7030 (tt0) REVERT: C 260 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8188 (mt-10) REVERT: C 272 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8322 (mm-40) REVERT: D 115 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8522 (mp) REVERT: D 207 ASN cc_start: 0.7782 (m-40) cc_final: 0.7355 (m-40) REVERT: F 272 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8428 (mm110) REVERT: G 221 MET cc_start: 0.7284 (mtp) cc_final: 0.7065 (mtp) outliers start: 24 outliers final: 20 residues processed: 203 average time/residue: 0.2538 time to fit residues: 75.5227 Evaluate side-chains 212 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 189 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.0570 chunk 42 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.150618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.109138 restraints weight = 14352.706| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.35 r_work: 0.2973 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13846 Z= 0.196 Angle : 0.467 7.572 18774 Z= 0.251 Chirality : 0.042 0.150 2303 Planarity : 0.003 0.055 2380 Dihedral : 4.603 28.622 1953 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.79 % Allowed : 19.64 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1778 helix: 0.81 (0.17), residues: 924 sheet: -0.27 (0.27), residues: 308 loop : -1.06 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 240 PHE 0.008 0.001 PHE F 235 TYR 0.013 0.001 TYR A 250 ARG 0.007 0.000 ARG D 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2846.59 seconds wall clock time: 52 minutes 17.28 seconds (3137.28 seconds total)