Starting phenix.real_space_refine on Mon Dec 30 15:15:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vyl_21463/12_2024/6vyl_21463.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vyl_21463/12_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/cci-nas-00/data/ceres_data/6vyl_21463/12_2024/6vyl_21463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vyl_21463/12_2024/6vyl_21463.map" model { file = "/net/cci-nas-00/data/ceres_data/6vyl_21463/12_2024/6vyl_21463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vyl_21463/12_2024/6vyl_21463.cif" } 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. Time to flip 14 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13671 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 4.96, per 1000 atoms: 0.36 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.9 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: 1.72 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: 4.60 Time building geometry restraints manager: 4.35 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: 0.00 - 1.32: 17019 1.32 - 2.64: 1415 2.64 - 3.97: 249 3.97 - 5.29: 63 5.29 - 6.61: 28 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 3.120 nonbonded pdb=" OD1 ASP D 199 " pdb=" NH2 ARG E 259 " model vdw 2.305 3.120 nonbonded pdb=" OE2 GLU F 220 " pdb=" OG1 THR F 222 " model vdw 2.306 3.040 nonbonded pdb=" OE2 GLU G 220 " pdb=" OG1 THR G 222 " model vdw 2.306 3.040 nonbonded pdb=" OE2 GLU D 220 " pdb=" OG1 THR D 222 " model vdw 2.306 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.380 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: 0.560 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 31.100 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.070 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:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.840 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 7 poor density : 302 time to evaluate : 1.862 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: 0.2807 time to fit residues: 123.6104 Evaluate side-chains 229 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 226 time to evaluate : 1.731 ------------------------------------------------------------------------------- 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: 0.9980 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 0.0030 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 210 GLN B 112 GLN C 112 GLN C 149 GLN D 112 GLN E 112 GLN F 112 GLN F 149 GLN F 210 GLN G 112 GLN G 210 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1553 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= 0.151 Angle : 0.503 5.527 18774 Z= 0.279 Chirality : 0.042 0.144 2303 Planarity : 0.005 0.062 2380 Dihedral : 5.730 34.026 1959 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.44 % Allowed : 13.32 % Favored : 85.23 % 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: -2.69 (0.18), residues: 1778 helix: -1.62 (0.15), residues: 917 sheet: -0.97 (0.28), residues: 259 loop : -2.11 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 251 PHE 0.011 0.001 PHE A 235 TYR 0.011 0.001 TYR F 250 ARG 0.005 0.000 ARG C 74 *********************** 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 243 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 1.687 Fit side-chains REVERT: A 245 ASP cc_start: 0.8089 (p0) cc_final: 0.7754 (p0) REVERT: A 272 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8612 (mm-40) REVERT: B 105 LEU cc_start: 0.6431 (mt) cc_final: 0.6115 (mp) REVERT: B 202 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8323 (ttmt) REVERT: B 272 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8221 (mm-40) REVERT: C 274 ASP cc_start: 0.8089 (t0) cc_final: 0.7516 (t0) REVERT: C 276 ASN cc_start: 0.8185 (m-40) cc_final: 0.7815 (m110) REVERT: D 74 ARG cc_start: 0.7124 (ttt180) cc_final: 0.6755 (ttp80) REVERT: D 80 PHE cc_start: 0.8300 (m-80) cc_final: 0.7968 (m-80) REVERT: D 115 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8604 (mp) REVERT: D 207 ASN cc_start: 0.7931 (m-40) cc_final: 0.7515 (m-40) REVERT: D 276 ASN cc_start: 0.8239 (m-40) cc_final: 0.7958 (m110) REVERT: E 74 ARG cc_start: 0.6792 (ttt180) cc_final: 0.6549 (ttp80) REVERT: E 272 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8349 (mm-40) REVERT: E 276 ASN cc_start: 0.8009 (m-40) cc_final: 0.7574 (m110) REVERT: F 56 MET cc_start: 0.7086 (mmt) cc_final: 0.6648 (mmp) REVERT: F 115 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8605 (mp) outliers start: 21 outliers final: 15 residues processed: 235 average time/residue: 0.3101 time to fit residues: 105.6386 Evaluate side-chains 219 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 222 THR 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 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 115 LEU Chi-restraints excluded: chain F residue 222 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 141 optimal weight: 0.2980 chunk 157 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 149 GLN C 149 GLN F 149 GLN F 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1902 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= 0.164 Angle : 0.468 6.179 18774 Z= 0.257 Chirality : 0.042 0.135 2303 Planarity : 0.004 0.058 2380 Dihedral : 5.341 33.751 1957 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.72 % Allowed : 16.14 % Favored : 82.14 % 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: -1.73 (0.19), residues: 1778 helix: -0.77 (0.17), residues: 917 sheet: -0.74 (0.26), residues: 308 loop : -1.74 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 240 PHE 0.009 0.001 PHE E 235 TYR 0.012 0.001 TYR A 250 ARG 0.006 0.000 ARG B 131 *********************** 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 236 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 1.585 Fit side-chains REVERT: A 149 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7473 (mp-120) REVERT: A 179 SER cc_start: 0.8039 (t) cc_final: 0.7835 (t) REVERT: B 272 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8312 (mm-40) REVERT: D 74 ARG cc_start: 0.7153 (ttt180) cc_final: 0.6782 (ttp80) REVERT: D 115 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8567 (mp) REVERT: D 207 ASN cc_start: 0.7917 (m-40) cc_final: 0.7491 (m-40) REVERT: D 276 ASN cc_start: 0.8264 (m-40) cc_final: 0.8023 (m110) REVERT: E 74 ARG cc_start: 0.6789 (ttt180) cc_final: 0.6574 (ttp80) REVERT: E 210 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8172 (mm110) REVERT: E 272 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8443 (mm-40) REVERT: E 276 ASN cc_start: 0.8072 (m-40) cc_final: 0.7621 (m110) REVERT: F 56 MET cc_start: 0.7098 (mmt) cc_final: 0.6610 (mmp) REVERT: F 115 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8622 (mp) REVERT: G 46 ARG cc_start: 0.7542 (mmm-85) cc_final: 0.7027 (mmt90) outliers start: 25 outliers final: 15 residues processed: 226 average time/residue: 0.2868 time to fit residues: 92.8089 Evaluate side-chains 216 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 222 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 225 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 222 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 222 THR 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: 7.9990 chunk 119 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 169 optimal weight: 0.0980 chunk 83 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13846 Z= 0.210 Angle : 0.478 7.868 18774 Z= 0.261 Chirality : 0.042 0.141 2303 Planarity : 0.004 0.060 2380 Dihedral : 5.306 42.522 1957 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.47 % Allowed : 17.93 % Favored : 79.60 % 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: -1.31 (0.20), residues: 1778 helix: -0.39 (0.17), residues: 924 sheet: -0.69 (0.27), residues: 308 loop : -1.54 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 240 PHE 0.007 0.001 PHE F 235 TYR 0.012 0.001 TYR A 250 ARG 0.005 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 240 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 1.515 Fit side-chains revert: symmetry clash REVERT: A 179 SER cc_start: 0.8029 (t) cc_final: 0.7811 (t) REVERT: B 272 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8381 (mm-40) REVERT: C 274 ASP cc_start: 0.8125 (t0) cc_final: 0.7578 (t0) REVERT: D 74 ARG cc_start: 0.7148 (ttt180) cc_final: 0.6792 (ttp80) REVERT: D 115 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8633 (mp) REVERT: D 207 ASN cc_start: 0.7929 (m-40) cc_final: 0.7512 (m-40) REVERT: E 74 ARG cc_start: 0.6866 (ttt180) cc_final: 0.6531 (ttp-170) REVERT: E 210 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8095 (mm110) REVERT: E 276 ASN cc_start: 0.8137 (m-40) cc_final: 0.7616 (m110) REVERT: F 56 MET cc_start: 0.7018 (mmt) cc_final: 0.6429 (mmp) REVERT: F 115 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8689 (mp) REVERT: G 46 ARG cc_start: 0.7546 (mmm-85) cc_final: 0.6952 (mmt90) outliers start: 36 outliers final: 23 residues processed: 229 average time/residue: 0.2683 time to fit residues: 88.8023 Evaluate side-chains 225 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.732 ------------------------------------------------------------------------------- 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 222 THR Chi-restraints excluded: chain B residue 171 ILE 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 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 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 115 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 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: 0.9990 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 86 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 272 GLN B 149 GLN F 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13846 Z= 0.209 Angle : 0.471 7.852 18774 Z= 0.256 Chirality : 0.042 0.150 2303 Planarity : 0.004 0.059 2380 Dihedral : 5.286 51.319 1957 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.92 % Allowed : 19.02 % Favored : 79.05 % 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: -0.98 (0.20), residues: 1778 helix: -0.11 (0.17), residues: 924 sheet: -0.78 (0.27), residues: 294 loop : -1.24 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 240 PHE 0.008 0.001 PHE A 235 TYR 0.013 0.001 TYR A 250 ARG 0.005 0.000 ARG D 131 *********************** 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 233 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 1.774 Fit side-chains revert: symmetry clash REVERT: A 212 GLU cc_start: 0.8663 (tp30) cc_final: 0.8437 (tp30) REVERT: B 126 MET cc_start: 0.7620 (mtt) cc_final: 0.7366 (mtt) REVERT: B 272 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8401 (mm-40) REVERT: C 46 ARG cc_start: 0.7423 (mmm-85) cc_final: 0.7194 (tpp80) REVERT: D 115 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8609 (mp) REVERT: D 207 ASN cc_start: 0.7944 (m-40) cc_final: 0.7514 (m-40) REVERT: E 74 ARG cc_start: 0.6875 (ttt180) cc_final: 0.6531 (ttp-170) REVERT: E 276 ASN cc_start: 0.8210 (m-40) cc_final: 0.7607 (m110) REVERT: F 56 MET cc_start: 0.7109 (mmt) cc_final: 0.6563 (mmp) REVERT: F 134 GLU cc_start: 0.7399 (tt0) cc_final: 0.7104 (tt0) REVERT: F 277 PHE cc_start: 0.7419 (m-10) cc_final: 0.7085 (m-80) REVERT: G 46 ARG cc_start: 0.7553 (mmm-85) cc_final: 0.6899 (mmt90) REVERT: G 134 GLU cc_start: 0.7437 (tt0) cc_final: 0.6944 (tt0) REVERT: G 180 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7440 (ttm170) outliers start: 28 outliers final: 18 residues processed: 221 average time/residue: 0.2754 time to fit residues: 87.2988 Evaluate side-chains 222 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 222 THR 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 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 82 LEU Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 222 THR 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: 4.9990 chunk 33 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 169 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 0.0370 chunk 88 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2456 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= 0.136 Angle : 0.448 9.510 18774 Z= 0.244 Chirality : 0.041 0.139 2303 Planarity : 0.004 0.059 2380 Dihedral : 5.130 55.477 1957 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.27 % Allowed : 18.75 % Favored : 78.98 % 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: -0.68 (0.20), residues: 1778 helix: 0.19 (0.17), residues: 924 sheet: -0.71 (0.27), residues: 294 loop : -1.16 (0.28), residues: 560 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 0.013 0.001 TYR A 250 ARG 0.010 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 239 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 1.646 Fit side-chains REVERT: A 212 GLU cc_start: 0.8623 (tp30) cc_final: 0.8400 (tp30) REVERT: C 272 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8357 (mm-40) REVERT: D 115 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8526 (mp) REVERT: D 207 ASN cc_start: 0.7839 (m-40) cc_final: 0.7412 (m-40) REVERT: D 272 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8192 (mm-40) REVERT: E 74 ARG cc_start: 0.6800 (ttt180) cc_final: 0.6558 (ttp-170) REVERT: E 272 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8284 (mm-40) REVERT: E 276 ASN cc_start: 0.8103 (m-40) cc_final: 0.7475 (m110) REVERT: F 56 MET cc_start: 0.6815 (mmt) cc_final: 0.6410 (mmp) REVERT: F 134 GLU cc_start: 0.7354 (tt0) cc_final: 0.7064 (tt0) REVERT: F 272 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8442 (mm-40) REVERT: G 180 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7380 (ttm170) REVERT: G 274 ASP cc_start: 0.7591 (t0) cc_final: 0.7265 (t0) outliers start: 33 outliers final: 20 residues processed: 230 average time/residue: 0.2935 time to fit residues: 96.0224 Evaluate side-chains 216 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL 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 82 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 171 ILE 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 171 ILE Chi-restraints excluded: chain G residue 180 ARG 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: 5.9990 chunk 96 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 149 GLN C 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2597 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= 0.146 Angle : 0.451 8.066 18774 Z= 0.244 Chirality : 0.041 0.161 2303 Planarity : 0.004 0.059 2380 Dihedral : 4.886 57.018 1955 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.27 % Allowed : 18.89 % Favored : 78.85 % 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: -0.49 (0.20), residues: 1778 helix: 0.36 (0.17), residues: 924 sheet: -0.67 (0.27), residues: 294 loop : -1.06 (0.29), residues: 560 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 0.012 0.001 TYR A 250 ARG 0.007 0.000 ARG D 131 *********************** 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 to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 1.641 Fit side-chains REVERT: A 212 GLU cc_start: 0.8627 (tp30) cc_final: 0.8410 (tp30) REVERT: B 126 MET cc_start: 0.7600 (mtt) cc_final: 0.7339 (mtt) REVERT: D 115 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8524 (mp) REVERT: D 207 ASN cc_start: 0.7782 (m-40) cc_final: 0.7382 (m-40) REVERT: E 74 ARG cc_start: 0.6791 (ttt180) cc_final: 0.6580 (ttp-170) REVERT: E 272 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8211 (mm-40) REVERT: F 56 MET cc_start: 0.6795 (mmt) cc_final: 0.6426 (mmp) REVERT: F 134 GLU cc_start: 0.7382 (tt0) cc_final: 0.7077 (tt0) REVERT: F 149 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8025 (mm-40) REVERT: G 134 GLU cc_start: 0.7450 (tt0) cc_final: 0.6976 (tt0) REVERT: G 180 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7400 (ttm170) REVERT: G 274 ASP cc_start: 0.7630 (t0) cc_final: 0.7307 (t0) outliers start: 33 outliers final: 23 residues processed: 222 average time/residue: 0.2727 time to fit residues: 87.2176 Evaluate side-chains 219 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE 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 82 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 171 ILE Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 78 ILE 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 180 ARG Chi-restraints excluded: chain G residue 222 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN G 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13846 Z= 0.183 Angle : 0.471 8.933 18774 Z= 0.252 Chirality : 0.042 0.192 2303 Planarity : 0.004 0.059 2380 Dihedral : 4.819 42.645 1955 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.92 % Allowed : 19.37 % 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: -0.41 (0.20), residues: 1778 helix: 0.43 (0.17), residues: 924 sheet: -0.66 (0.27), residues: 294 loop : -1.03 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 240 PHE 0.010 0.001 PHE F 277 TYR 0.013 0.001 TYR A 250 ARG 0.008 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 220 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 1.477 Fit side-chains REVERT: B 126 MET cc_start: 0.7602 (mtt) cc_final: 0.7355 (mtt) REVERT: D 115 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8546 (mp) REVERT: D 149 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8104 (mm-40) REVERT: D 207 ASN cc_start: 0.7796 (m-40) cc_final: 0.7373 (m-40) REVERT: E 74 ARG cc_start: 0.6803 (ttt180) cc_final: 0.6570 (ttp-170) REVERT: E 272 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8269 (mm-40) REVERT: F 56 MET cc_start: 0.6788 (mmt) cc_final: 0.6408 (mmp) REVERT: F 134 GLU cc_start: 0.7450 (tt0) cc_final: 0.7167 (tt0) REVERT: F 149 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8176 (mm-40) REVERT: G 134 GLU cc_start: 0.7447 (tt0) cc_final: 0.7153 (tt0) REVERT: G 274 ASP cc_start: 0.7593 (t0) cc_final: 0.7297 (t0) outliers start: 28 outliers final: 26 residues processed: 208 average time/residue: 0.2680 time to fit residues: 80.2310 Evaluate side-chains 217 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 78 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 E residue 49 SER Chi-restraints excluded: chain E residue 82 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 171 ILE Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 222 THR 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 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: 0.9980 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN B 149 GLN C 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2744 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= 0.153 Angle : 0.457 7.285 18774 Z= 0.246 Chirality : 0.041 0.138 2303 Planarity : 0.004 0.059 2380 Dihedral : 4.630 29.083 1953 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.85 % Allowed : 19.37 % Favored : 78.78 % 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: -0.24 (0.20), residues: 1778 helix: 0.62 (0.17), residues: 924 sheet: -0.65 (0.28), residues: 294 loop : -1.01 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 240 PHE 0.008 0.001 PHE E 235 TYR 0.013 0.001 TYR A 250 ARG 0.007 0.000 ARG D 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 220 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 1.595 Fit side-chains REVERT: A 212 GLU cc_start: 0.8624 (tp30) cc_final: 0.8335 (tp30) REVERT: B 126 MET cc_start: 0.7593 (mtt) cc_final: 0.7331 (mtt) REVERT: C 273 MET cc_start: 0.8105 (tpp) cc_final: 0.7882 (tpp) REVERT: D 115 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8532 (mp) REVERT: D 207 ASN cc_start: 0.7758 (m-40) cc_final: 0.7325 (m-40) REVERT: D 272 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8430 (mm-40) REVERT: E 74 ARG cc_start: 0.6783 (ttt180) cc_final: 0.6563 (ttp-170) REVERT: F 56 MET cc_start: 0.6717 (mmt) cc_final: 0.6369 (mmp) REVERT: F 134 GLU cc_start: 0.7418 (tt0) cc_final: 0.7145 (tt0) REVERT: F 149 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8184 (mm-40) REVERT: G 134 GLU cc_start: 0.7437 (tt0) cc_final: 0.7137 (tt0) REVERT: G 274 ASP cc_start: 0.7625 (t0) cc_final: 0.7300 (t0) outliers start: 27 outliers final: 25 residues processed: 210 average time/residue: 0.2680 time to fit residues: 81.6419 Evaluate side-chains 215 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 222 THR 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 222 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 275 VAL 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 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 171 ILE Chi-restraints excluded: chain G residue 222 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 14 optimal weight: 0.0770 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 overall best weight: 1.2740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN C 149 GLN E 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13846 Z= 0.186 Angle : 0.470 6.992 18774 Z= 0.252 Chirality : 0.042 0.140 2303 Planarity : 0.004 0.059 2380 Dihedral : 4.657 28.747 1953 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % 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: -0.19 (0.20), residues: 1778 helix: 0.66 (0.17), residues: 924 sheet: -0.63 (0.28), residues: 294 loop : -0.98 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 240 PHE 0.008 0.001 PHE E 235 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 218 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 1.680 Fit side-chains REVERT: A 212 GLU cc_start: 0.8676 (tp30) cc_final: 0.8392 (tp30) REVERT: B 126 MET cc_start: 0.7600 (mtt) cc_final: 0.7379 (mtt) REVERT: D 55 LEU cc_start: 0.7694 (tt) cc_final: 0.7262 (tp) REVERT: D 115 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8537 (mp) REVERT: D 134 GLU cc_start: 0.6833 (tt0) cc_final: 0.6532 (tt0) REVERT: D 207 ASN cc_start: 0.7750 (m-40) cc_final: 0.7347 (m-40) REVERT: D 272 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8407 (mm-40) REVERT: E 74 ARG cc_start: 0.6799 (ttt180) cc_final: 0.6558 (ttp80) REVERT: F 56 MET cc_start: 0.6900 (mmt) cc_final: 0.6441 (mmp) REVERT: F 134 GLU cc_start: 0.7418 (tt0) cc_final: 0.7130 (tt0) REVERT: F 149 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8178 (mm-40) REVERT: G 134 GLU cc_start: 0.7461 (tt0) cc_final: 0.7142 (tt0) REVERT: G 274 ASP cc_start: 0.7592 (t0) cc_final: 0.7317 (t0) outliers start: 29 outliers final: 28 residues processed: 207 average time/residue: 0.2699 time to fit residues: 81.5038 Evaluate side-chains 217 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 171 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 89 VAL 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 171 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 275 VAL 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 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 171 ILE Chi-restraints excluded: chain G residue 222 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 142 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.151789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.110678 restraints weight = 14316.241| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.38 r_work: 0.2991 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 13846 Z= 0.143 Angle : 0.458 7.068 18774 Z= 0.246 Chirality : 0.041 0.138 2303 Planarity : 0.004 0.059 2380 Dihedral : 4.551 27.942 1953 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.79 % Allowed : 19.23 % 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: -0.02 (0.21), residues: 1778 helix: 0.82 (0.17), residues: 924 sheet: -0.59 (0.28), residues: 294 loop : -0.94 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 251 PHE 0.009 0.001 PHE E 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: 2848.40 seconds wall clock time: 53 minutes 17.81 seconds (3197.81 seconds total)