Starting phenix.real_space_refine on Thu Jul 31 11:02:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vyl_21463/07_2025/6vyl_21463.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vyl_21463/07_2025/6vyl_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_21463/07_2025/6vyl_21463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vyl_21463/07_2025/6vyl_21463.map" model { file = "/net/cci-nas-00/data/ceres_data/6vyl_21463/07_2025/6vyl_21463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vyl_21463/07_2025/6vyl_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 4.95, 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: 3.26 Conformation dependent library (CDL) restraints added in 1.8 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: 1.52 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: 4.13 Time building geometry restraints manager: 3.88 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 0.200 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 29.310 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.530 ------------------------------------------------------------------------------- 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= 0.351 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 Details of bonding type rmsd hydrogen bonds : bond 0.11307 ( 769) hydrogen bonds : angle 5.78350 ( 2241) covalent geometry : bond 0.00840 (13846) covalent geometry : angle 0.84652 (18774) *********************** 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 : 1.681 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: 0.2706 time to fit residues: 119.9279 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 : 1.476 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.150139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.109774 restraints weight = 14340.130| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.36 r_work: 0.2987 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1549 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= 0.110 Angle : 0.501 5.528 18774 Z= 0.278 Chirality : 0.042 0.145 2303 Planarity : 0.005 0.062 2380 Dihedral : 5.735 34.027 1959 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.44 % Allowed : 13.26 % Favored : 85.30 % 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: -1.61 (0.15), residues: 917 sheet: -0.98 (0.26), residues: 273 loop : -2.15 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 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 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 769) hydrogen bonds : angle 4.07803 ( 2241) covalent geometry : bond 0.00231 (13846) covalent geometry : angle 0.50149 (18774) *********************** 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 : 1.571 Fit side-chains REVERT: A 74 ARG cc_start: 0.6440 (ttt180) cc_final: 0.6135 (ttp80) REVERT: A 245 ASP cc_start: 0.8494 (p0) cc_final: 0.7800 (p0) REVERT: A 272 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8703 (mm-40) REVERT: B 105 LEU cc_start: 0.6258 (mt) cc_final: 0.5947 (mp) REVERT: B 128 ARG cc_start: 0.8213 (mtp-110) cc_final: 0.7975 (mtp-110) REVERT: B 202 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8233 (ttmt) REVERT: B 272 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8310 (mm-40) REVERT: C 134 GLU cc_start: 0.8119 (tt0) cc_final: 0.7740 (tt0) REVERT: C 149 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8600 (mp10) REVERT: C 274 ASP cc_start: 0.8706 (t0) cc_final: 0.7811 (t0) REVERT: C 276 ASN cc_start: 0.8287 (m-40) cc_final: 0.7782 (m110) REVERT: D 74 ARG cc_start: 0.6765 (ttt180) cc_final: 0.6118 (ttp80) REVERT: D 80 PHE cc_start: 0.7591 (m-80) cc_final: 0.7350 (m-80) REVERT: D 115 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8576 (mp) REVERT: D 155 MET cc_start: 0.8836 (ptm) cc_final: 0.8625 (ptp) REVERT: D 207 ASN cc_start: 0.8278 (m-40) cc_final: 0.7860 (m-40) REVERT: D 210 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8575 (mm110) REVERT: D 276 ASN cc_start: 0.8350 (m-40) cc_final: 0.8037 (m110) REVERT: E 74 ARG cc_start: 0.6419 (ttt180) cc_final: 0.5912 (ttp80) REVERT: E 272 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8399 (mm-40) REVERT: E 276 ASN cc_start: 0.8150 (m-40) cc_final: 0.7687 (m110) REVERT: F 56 MET cc_start: 0.6931 (mmt) cc_final: 0.6460 (mmp) REVERT: F 74 ARG cc_start: 0.6631 (ttt180) cc_final: 0.6194 (ttp80) REVERT: F 128 ARG cc_start: 0.8460 (mtm110) cc_final: 0.8260 (mtp-110) outliers start: 21 outliers final: 15 residues processed: 235 average time/residue: 0.2809 time to fit residues: 94.7816 Evaluate side-chains 221 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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 149 GLN 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 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: 6.9990 chunk 71 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 F 149 GLN F 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.146538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.105677 restraints weight = 14560.025| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.36 r_work: 0.3127 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13846 Z= 0.193 Angle : 0.520 6.148 18774 Z= 0.283 Chirality : 0.044 0.144 2303 Planarity : 0.004 0.058 2380 Dihedral : 5.568 42.848 1957 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.13 % Allowed : 16.62 % Favored : 81.25 % 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: -1.86 (0.19), residues: 1778 helix: -0.87 (0.16), residues: 924 sheet: -0.91 (0.26), residues: 308 loop : -1.73 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 240 PHE 0.008 0.001 PHE G 268 TYR 0.012 0.001 TYR A 250 ARG 0.007 0.000 ARG D 131 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 769) hydrogen bonds : angle 3.91391 ( 2241) covalent geometry : bond 0.00464 (13846) covalent geometry : angle 0.52020 (18774) *********************** 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 252 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 1.645 Fit side-chains REVERT: A 74 ARG cc_start: 0.6547 (ttt180) cc_final: 0.6269 (ttp80) REVERT: A 131 ARG cc_start: 0.7881 (mtt90) cc_final: 0.7380 (mtp-110) REVERT: A 149 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7742 (mp-120) REVERT: B 272 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8539 (mm-40) REVERT: C 131 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7684 (mtp-110) REVERT: C 134 GLU cc_start: 0.8095 (tt0) cc_final: 0.7634 (tt0) REVERT: D 74 ARG cc_start: 0.6968 (ttt180) cc_final: 0.6358 (ttp80) REVERT: D 115 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8694 (mp) REVERT: D 134 GLU cc_start: 0.7665 (tt0) cc_final: 0.7351 (tt0) REVERT: D 207 ASN cc_start: 0.8371 (m-40) cc_final: 0.7975 (m-40) REVERT: E 74 ARG cc_start: 0.6530 (ttt180) cc_final: 0.6036 (ttp80) REVERT: E 276 ASN cc_start: 0.8471 (m-40) cc_final: 0.8054 (m110) REVERT: F 56 MET cc_start: 0.7007 (mmt) cc_final: 0.6425 (mmp) REVERT: F 74 ARG cc_start: 0.6726 (ttt180) cc_final: 0.6332 (ttp80) REVERT: F 134 GLU cc_start: 0.8134 (tt0) cc_final: 0.7808 (tt0) REVERT: F 137 ASP cc_start: 0.8257 (t0) cc_final: 0.7994 (t0) REVERT: G 46 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7012 (mmt90) REVERT: G 134 GLU cc_start: 0.8147 (tt0) cc_final: 0.7625 (tt0) outliers start: 31 outliers final: 15 residues processed: 240 average time/residue: 0.2721 time to fit residues: 93.4010 Evaluate side-chains 231 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 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 222 THR Chi-restraints excluded: chain B residue 222 THR 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 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 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 161 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 108 optimal weight: 0.3980 chunk 166 optimal weight: 0.0970 chunk 123 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.184726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.146481 restraints weight = 13785.805| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.82 r_work: 0.3009 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13846 Z= 0.095 Angle : 0.457 5.258 18774 Z= 0.251 Chirality : 0.041 0.134 2303 Planarity : 0.004 0.061 2380 Dihedral : 5.104 41.355 1955 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.51 % Allowed : 18.34 % Favored : 80.15 % 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: -1.26 (0.20), residues: 1778 helix: -0.34 (0.17), residues: 917 sheet: -0.79 (0.27), residues: 294 loop : -1.44 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 240 PHE 0.032 0.001 PHE D 80 TYR 0.013 0.001 TYR A 250 ARG 0.005 0.000 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 769) hydrogen bonds : angle 3.67280 ( 2241) covalent geometry : bond 0.00198 (13846) covalent geometry : angle 0.45692 (18774) *********************** 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 235 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 3.844 Fit side-chains REVERT: A 74 ARG cc_start: 0.6517 (ttt180) cc_final: 0.6136 (ttp80) REVERT: A 131 ARG cc_start: 0.7623 (mtt90) cc_final: 0.6821 (mtp-110) REVERT: C 131 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7398 (mtp-110) REVERT: C 134 GLU cc_start: 0.7980 (tt0) cc_final: 0.7333 (tt0) REVERT: C 272 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8409 (mm-40) REVERT: D 74 ARG cc_start: 0.6827 (ttt180) cc_final: 0.6226 (ttp80) REVERT: D 115 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8623 (mp) REVERT: D 131 ARG cc_start: 0.7787 (mtp-110) cc_final: 0.7568 (mtp-110) REVERT: D 207 ASN cc_start: 0.8176 (m-40) cc_final: 0.7776 (m-40) REVERT: D 276 ASN cc_start: 0.8362 (m-40) cc_final: 0.8133 (m110) REVERT: E 74 ARG cc_start: 0.6425 (ttt180) cc_final: 0.5858 (ttp-170) REVERT: E 210 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8454 (mm110) REVERT: E 276 ASN cc_start: 0.8209 (m-40) cc_final: 0.7597 (m110) REVERT: F 56 MET cc_start: 0.6980 (mmt) cc_final: 0.6442 (mmp) REVERT: F 74 ARG cc_start: 0.6511 (ttt180) cc_final: 0.6274 (ttp80) REVERT: F 137 ASP cc_start: 0.8314 (t0) cc_final: 0.8085 (t0) REVERT: G 46 ARG cc_start: 0.7569 (mmm-85) cc_final: 0.6865 (mmt90) REVERT: G 131 ARG cc_start: 0.7969 (mtt90) cc_final: 0.7255 (mtp-110) outliers start: 22 outliers final: 13 residues processed: 228 average time/residue: 0.3307 time to fit residues: 109.2830 Evaluate side-chains 219 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 80 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 103 optimal weight: 0.0070 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 149 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 114 optimal weight: 0.0060 chunk 4 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN F 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.150510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.109046 restraints weight = 14369.154| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.47 r_work: 0.2964 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13846 Z= 0.101 Angle : 0.444 7.812 18774 Z= 0.242 Chirality : 0.041 0.137 2303 Planarity : 0.004 0.058 2380 Dihedral : 4.959 45.389 1955 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.85 % Allowed : 19.16 % Favored : 78.98 % 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: -0.88 (0.20), residues: 1778 helix: 0.02 (0.17), residues: 917 sheet: -0.71 (0.27), residues: 294 loop : -1.29 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 240 PHE 0.019 0.001 PHE D 80 TYR 0.012 0.001 TYR C 250 ARG 0.004 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 769) hydrogen bonds : angle 3.57977 ( 2241) covalent geometry : bond 0.00217 (13846) covalent geometry : angle 0.44374 (18774) *********************** 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 236 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 1.558 Fit side-chains REVERT: A 74 ARG cc_start: 0.6470 (ttt180) cc_final: 0.6111 (ttp80) REVERT: A 272 GLN cc_start: 0.9272 (mm-40) cc_final: 0.9064 (mm110) REVERT: A 273 MET cc_start: 0.8988 (mmm) cc_final: 0.8781 (mmm) REVERT: C 46 ARG cc_start: 0.7487 (mmm-85) cc_final: 0.7159 (tpp80) REVERT: C 131 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7526 (mtp-110) REVERT: C 134 GLU cc_start: 0.8155 (tt0) cc_final: 0.7475 (tt0) REVERT: C 272 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8457 (mm-40) REVERT: D 74 ARG cc_start: 0.6776 (ttt180) cc_final: 0.6336 (ttp80) REVERT: D 115 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8628 (mp) REVERT: D 207 ASN cc_start: 0.8123 (m-40) cc_final: 0.7741 (m-40) REVERT: E 74 ARG cc_start: 0.6353 (ttt180) cc_final: 0.5812 (ttp-170) REVERT: E 276 ASN cc_start: 0.8516 (m-40) cc_final: 0.8165 (m110) REVERT: F 56 MET cc_start: 0.6775 (mmt) cc_final: 0.6263 (mmp) REVERT: F 74 ARG cc_start: 0.6465 (ttt180) cc_final: 0.6252 (ttp80) REVERT: F 137 ASP cc_start: 0.8404 (t0) cc_final: 0.8189 (t0) REVERT: F 272 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8790 (mm-40) REVERT: F 277 PHE cc_start: 0.7939 (m-10) cc_final: 0.7554 (m-80) REVERT: G 46 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.6781 (mmt90) REVERT: G 131 ARG cc_start: 0.8003 (mtt90) cc_final: 0.7151 (mtp-110) REVERT: G 134 GLU cc_start: 0.8400 (tt0) cc_final: 0.7783 (tt0) outliers start: 27 outliers final: 20 residues processed: 225 average time/residue: 0.3427 time to fit residues: 109.7544 Evaluate side-chains 222 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL 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 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 273 MET Chi-restraints excluded: chain E residue 275 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 150 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 169 optimal weight: 0.0030 chunk 127 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 35 optimal weight: 0.0070 chunk 88 optimal weight: 3.9990 overall best weight: 1.8014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN F 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.148013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.107117 restraints weight = 14668.421| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.39 r_work: 0.2941 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13846 Z= 0.156 Angle : 0.470 5.728 18774 Z= 0.256 Chirality : 0.042 0.143 2303 Planarity : 0.004 0.061 2380 Dihedral : 5.065 55.701 1955 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.54 % Allowed : 18.54 % Favored : 78.91 % 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: -0.79 (0.20), residues: 1778 helix: 0.06 (0.17), residues: 924 sheet: -0.72 (0.28), residues: 294 loop : -1.17 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 240 PHE 0.015 0.001 PHE D 80 TYR 0.012 0.001 TYR A 250 ARG 0.008 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 769) hydrogen bonds : angle 3.64622 ( 2241) covalent geometry : bond 0.00370 (13846) covalent geometry : angle 0.47019 (18774) *********************** 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 244 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 1.661 Fit side-chains REVERT: A 74 ARG cc_start: 0.6501 (ttt180) cc_final: 0.6150 (ttp80) REVERT: C 74 ARG cc_start: 0.6476 (ttp80) cc_final: 0.6169 (ttp80) REVERT: C 131 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7520 (mtp-110) REVERT: C 134 GLU cc_start: 0.8234 (tt0) cc_final: 0.7534 (tt0) REVERT: C 272 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8497 (mm-40) REVERT: D 115 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8570 (mp) REVERT: D 134 GLU cc_start: 0.7963 (tt0) cc_final: 0.7562 (tt0) REVERT: D 207 ASN cc_start: 0.8106 (m-40) cc_final: 0.7712 (m-40) REVERT: E 74 ARG cc_start: 0.6483 (ttt180) cc_final: 0.5977 (ttp-170) REVERT: E 276 ASN cc_start: 0.8535 (m-40) cc_final: 0.8161 (m110) REVERT: F 56 MET cc_start: 0.6898 (mmt) cc_final: 0.6341 (mmp) REVERT: F 74 ARG cc_start: 0.6531 (ttt180) cc_final: 0.6278 (ttp80) REVERT: F 134 GLU cc_start: 0.8398 (tt0) cc_final: 0.7817 (tt0) REVERT: F 277 PHE cc_start: 0.7925 (m-10) cc_final: 0.7551 (m-80) REVERT: G 134 GLU cc_start: 0.8425 (tt0) cc_final: 0.7854 (tt0) outliers start: 37 outliers final: 28 residues processed: 232 average time/residue: 0.3188 time to fit residues: 107.0651 Evaluate side-chains 234 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 171 ILE 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 157 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 151 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 12 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 85 optimal weight: 0.0770 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 G 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.150780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.108884 restraints weight = 14479.429| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.49 r_work: 0.2961 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13846 Z= 0.094 Angle : 0.444 8.535 18774 Z= 0.241 Chirality : 0.041 0.147 2303 Planarity : 0.004 0.059 2380 Dihedral : 4.895 57.602 1955 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.34 % Allowed : 18.68 % 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: -0.54 (0.20), residues: 1778 helix: 0.35 (0.17), residues: 917 sheet: -0.68 (0.27), residues: 294 loop : -1.16 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 240 PHE 0.017 0.001 PHE D 80 TYR 0.013 0.001 TYR A 250 ARG 0.006 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 769) hydrogen bonds : angle 3.54127 ( 2241) covalent geometry : bond 0.00200 (13846) covalent geometry : angle 0.44442 (18774) *********************** 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 235 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 1.669 Fit side-chains REVERT: A 74 ARG cc_start: 0.6608 (ttt180) cc_final: 0.6210 (ttp80) REVERT: A 131 ARG cc_start: 0.7624 (mtt90) cc_final: 0.6951 (mtp-110) REVERT: B 128 ARG cc_start: 0.8353 (mtt90) cc_final: 0.7996 (mtp-110) REVERT: C 74 ARG cc_start: 0.6395 (ttp80) cc_final: 0.6184 (ttp80) REVERT: C 131 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7514 (mtp-110) REVERT: C 134 GLU cc_start: 0.8190 (tt0) cc_final: 0.7485 (tt0) REVERT: C 272 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8519 (mm-40) REVERT: D 115 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8517 (mp) REVERT: D 134 GLU cc_start: 0.7969 (tt0) cc_final: 0.7544 (tt0) REVERT: D 207 ASN cc_start: 0.8106 (m-40) cc_final: 0.7750 (m-40) REVERT: D 210 GLN cc_start: 0.8837 (mm110) cc_final: 0.8591 (mm-40) REVERT: D 272 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8747 (mm110) REVERT: E 74 ARG cc_start: 0.6392 (ttt180) cc_final: 0.5943 (ttp-170) REVERT: E 276 ASN cc_start: 0.8465 (m-40) cc_final: 0.8057 (m110) REVERT: F 56 MET cc_start: 0.6662 (mmt) cc_final: 0.6247 (mmp) REVERT: F 74 ARG cc_start: 0.6461 (ttt180) cc_final: 0.6252 (ttp80) REVERT: F 134 GLU cc_start: 0.8441 (tt0) cc_final: 0.7883 (tt0) REVERT: F 277 PHE cc_start: 0.7887 (m-10) cc_final: 0.7627 (m-10) REVERT: G 131 ARG cc_start: 0.7876 (mtt90) cc_final: 0.7157 (mtp-110) REVERT: G 134 GLU cc_start: 0.8410 (tt0) cc_final: 0.7776 (tt0) outliers start: 34 outliers final: 26 residues processed: 224 average time/residue: 0.2719 time to fit residues: 87.5878 Evaluate side-chains 225 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 B residue 78 ILE 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 157 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 D residue 225 LEU Chi-restraints excluded: chain E residue 82 LEU 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 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 222 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 42 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 151 optimal weight: 20.0000 chunk 3 optimal weight: 0.0670 chunk 139 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.190121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.151390 restraints weight = 13756.041| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.84 r_work: 0.3362 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2657 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= 0.090 Angle : 0.439 6.809 18774 Z= 0.238 Chirality : 0.041 0.165 2303 Planarity : 0.004 0.059 2380 Dihedral : 4.741 46.205 1955 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.65 % Allowed : 19.51 % 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: -0.33 (0.20), residues: 1778 helix: 0.55 (0.17), residues: 917 sheet: -0.61 (0.28), residues: 294 loop : -1.11 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP G 240 PHE 0.015 0.001 PHE D 80 TYR 0.012 0.000 TYR A 250 ARG 0.007 0.000 ARG D 131 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 769) hydrogen bonds : angle 3.50280 ( 2241) covalent geometry : bond 0.00191 (13846) covalent geometry : angle 0.43949 (18774) *********************** 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 224 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 1.587 Fit side-chains REVERT: A 74 ARG cc_start: 0.6776 (ttt180) cc_final: 0.6432 (ttp80) REVERT: A 212 GLU cc_start: 0.8805 (tp30) cc_final: 0.8604 (tp30) REVERT: C 131 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7685 (mtp-110) REVERT: C 134 GLU cc_start: 0.8060 (tt0) cc_final: 0.7554 (tt0) REVERT: C 272 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8852 (mm-40) REVERT: D 115 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8567 (mp) REVERT: D 134 GLU cc_start: 0.7618 (tt0) cc_final: 0.7286 (tt0) REVERT: D 149 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8273 (mm-40) REVERT: D 207 ASN cc_start: 0.8174 (m-40) cc_final: 0.7803 (m-40) REVERT: E 74 ARG cc_start: 0.6504 (ttt180) cc_final: 0.6054 (ttp-170) REVERT: E 276 ASN cc_start: 0.8558 (m-40) cc_final: 0.8206 (m110) REVERT: F 56 MET cc_start: 0.6639 (mmt) cc_final: 0.6239 (mmp) REVERT: F 74 ARG cc_start: 0.6715 (ttt180) cc_final: 0.6492 (ttp80) REVERT: F 134 GLU cc_start: 0.8211 (tt0) cc_final: 0.7864 (tt0) REVERT: F 149 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8297 (mm-40) REVERT: G 131 ARG cc_start: 0.7974 (mtt90) cc_final: 0.7413 (mtp-110) REVERT: G 134 GLU cc_start: 0.8237 (tt0) cc_final: 0.7809 (tt0) REVERT: G 274 ASP cc_start: 0.8575 (t0) cc_final: 0.8133 (t0) outliers start: 24 outliers final: 22 residues processed: 218 average time/residue: 0.2713 time to fit residues: 85.0302 Evaluate side-chains 219 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 B residue 171 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 157 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 D residue 225 LEU Chi-restraints excluded: chain E residue 82 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 16 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 53 optimal weight: 0.0060 chunk 37 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 overall best weight: 2.6002 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.146670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.105575 restraints weight = 14505.996| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.38 r_work: 0.2915 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13846 Z= 0.206 Angle : 0.517 7.519 18774 Z= 0.276 Chirality : 0.044 0.142 2303 Planarity : 0.004 0.059 2380 Dihedral : 4.952 30.200 1955 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.06 % Allowed : 19.37 % 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: -0.51 (0.20), residues: 1778 helix: 0.33 (0.17), residues: 924 sheet: -0.67 (0.28), residues: 294 loop : -1.07 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 240 PHE 0.011 0.002 PHE D 80 TYR 0.014 0.001 TYR A 250 ARG 0.009 0.000 ARG D 131 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 769) hydrogen bonds : angle 3.73444 ( 2241) covalent geometry : bond 0.00492 (13846) covalent geometry : angle 0.51726 (18774) *********************** 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 235 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 1.481 Fit side-chains REVERT: A 74 ARG cc_start: 0.6684 (ttt180) cc_final: 0.6311 (ttp80) REVERT: B 128 ARG cc_start: 0.8455 (mtt90) cc_final: 0.8059 (mtp-110) REVERT: B 131 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7063 (ttp-110) REVERT: C 131 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7471 (mtp-110) REVERT: C 134 GLU cc_start: 0.8324 (tt0) cc_final: 0.7599 (tt0) REVERT: D 80 PHE cc_start: 0.7523 (m-80) cc_final: 0.7147 (m-80) REVERT: D 115 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8603 (mp) REVERT: D 149 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8172 (mm-40) REVERT: D 207 ASN cc_start: 0.8085 (m-40) cc_final: 0.7720 (m-40) REVERT: E 74 ARG cc_start: 0.6450 (ttt180) cc_final: 0.5931 (ttp80) REVERT: E 276 ASN cc_start: 0.8596 (m-40) cc_final: 0.8130 (m110) REVERT: F 56 MET cc_start: 0.6767 (mmt) cc_final: 0.6241 (mmp) REVERT: F 74 ARG cc_start: 0.6589 (ttt180) cc_final: 0.6380 (ttp80) REVERT: F 134 GLU cc_start: 0.8498 (tt0) cc_final: 0.7929 (tt0) REVERT: F 149 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8320 (mm-40) REVERT: G 131 ARG cc_start: 0.7841 (mtt90) cc_final: 0.7145 (mtp-110) REVERT: G 134 GLU cc_start: 0.8477 (tt0) cc_final: 0.7793 (tt0) outliers start: 30 outliers final: 28 residues processed: 225 average time/residue: 0.2616 time to fit residues: 84.8310 Evaluate side-chains 229 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 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 155 MET Chi-restraints excluded: chain C residue 157 THR 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 D residue 222 THR 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 65 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 37 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 172 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 100 optimal weight: 0.2980 chunk 7 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.150343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.109322 restraints weight = 14387.084| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.38 r_work: 0.2970 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2693 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= 0.095 Angle : 0.462 8.042 18774 Z= 0.248 Chirality : 0.041 0.138 2303 Planarity : 0.004 0.061 2380 Dihedral : 4.662 28.546 1953 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.65 % Allowed : 19.71 % Favored : 78.64 % 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: -0.26 (0.21), residues: 1778 helix: 0.58 (0.17), residues: 924 sheet: -0.63 (0.28), residues: 294 loop : -0.99 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 240 PHE 0.014 0.001 PHE D 80 TYR 0.013 0.001 TYR A 250 ARG 0.008 0.000 ARG D 131 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 769) hydrogen bonds : angle 3.56490 ( 2241) covalent geometry : bond 0.00199 (13846) covalent geometry : angle 0.46208 (18774) ********************** 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 223 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 1.632 Fit side-chains REVERT: A 74 ARG cc_start: 0.6612 (ttt180) cc_final: 0.6281 (ttp80) REVERT: A 212 GLU cc_start: 0.8920 (tp30) cc_final: 0.8675 (tp30) REVERT: B 128 ARG cc_start: 0.8374 (mtt90) cc_final: 0.7987 (mtp-110) REVERT: B 131 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7014 (mtp-110) REVERT: C 131 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7372 (mtp-110) REVERT: C 134 GLU cc_start: 0.8239 (tt0) cc_final: 0.7450 (tt0) REVERT: C 272 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8428 (mm-40) REVERT: D 115 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8476 (mp) REVERT: D 149 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8177 (mm-40) REVERT: D 207 ASN cc_start: 0.7932 (m-40) cc_final: 0.7533 (m-40) REVERT: D 272 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8258 (mm-40) REVERT: E 74 ARG cc_start: 0.6374 (ttt180) cc_final: 0.5873 (ttp80) REVERT: E 276 ASN cc_start: 0.8399 (m-40) cc_final: 0.7887 (m110) REVERT: F 56 MET cc_start: 0.6742 (mmt) cc_final: 0.6243 (mmp) REVERT: F 74 ARG cc_start: 0.6609 (ttt180) cc_final: 0.6395 (ttp80) REVERT: F 134 GLU cc_start: 0.8417 (tt0) cc_final: 0.7837 (tt0) REVERT: F 149 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8308 (mm-40) REVERT: F 277 PHE cc_start: 0.7854 (m-10) cc_final: 0.7645 (m-10) REVERT: G 131 ARG cc_start: 0.7744 (mtt90) cc_final: 0.7047 (mtp-110) REVERT: G 134 GLU cc_start: 0.8374 (tt0) cc_final: 0.7673 (tt0) outliers start: 24 outliers final: 21 residues processed: 217 average time/residue: 0.2679 time to fit residues: 83.7407 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 : 1.450 ------------------------------------------------------------------------------- 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 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 E residue 275 VAL Chi-restraints excluded: chain F residue 65 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 54 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 157 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.151171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.109950 restraints weight = 14500.383| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.41 r_work: 0.2978 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 13846 Z= 0.097 Angle : 0.453 7.643 18774 Z= 0.245 Chirality : 0.041 0.137 2303 Planarity : 0.004 0.059 2380 Dihedral : 4.584 28.673 1953 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.58 % Allowed : 19.78 % Favored : 78.64 % 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: -0.09 (0.21), residues: 1778 helix: 0.74 (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 D 251 PHE 0.014 0.001 PHE D 80 TYR 0.013 0.001 TYR A 250 ARG 0.010 0.000 ARG D 131 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 769) hydrogen bonds : angle 3.53875 ( 2241) covalent geometry : bond 0.00215 (13846) covalent geometry : angle 0.45321 (18774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6911.19 seconds wall clock time: 123 minutes 28.03 seconds (7408.03 seconds total)