Starting phenix.real_space_refine on Wed Mar 4 11:51:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vyl_21463/03_2026/6vyl_21463.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vyl_21463/03_2026/6vyl_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 { model { file = "/net/cci-nas-00/data/ceres_data/6vyl_21463/03_2026/6vyl_21463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vyl_21463/03_2026/6vyl_21463.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vyl_21463/03_2026/6vyl_21463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vyl_21463/03_2026/6vyl_21463.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: B, C, D, E, F, G Time building chain proxies: 1.93, per 1000 atoms: 0.14 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: 1.21 Conformation dependent library (CDL) restraints added in 724.5 milliseconds 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: 0.49 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: 2.17 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.170 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.250 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG C 238 TYR 0.009 0.002 TYR D 250 PHE 0.013 0.003 PHE D 178 TRP 0.005 0.001 TRP F 251 Details of bonding type rmsd covalent geometry : bond 0.00840 (13846) covalent geometry : angle 0.84652 (18774) hydrogen bonds : bond 0.11307 ( 769) hydrogen bonds : angle 5.78350 ( 2241) *********************** 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 : 0.508 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: 0.7267 (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: 0.7330 (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: 0.7588 (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: 0.1246 time to fit residues: 55.8512 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 : 0.521 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.146578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.105930 restraints weight = 14581.892| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.37 r_work: 0.3164 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13846 Z= 0.188 Angle : 0.549 5.593 18774 Z= 0.301 Chirality : 0.044 0.145 2303 Planarity : 0.005 0.062 2380 Dihedral : 5.919 39.639 1959 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.13 % Allowed : 13.53 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.18), residues: 1778 helix: -1.74 (0.15), residues: 917 sheet: -1.16 (0.28), residues: 259 loop : -2.10 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 128 TYR 0.009 0.001 TYR F 250 PHE 0.008 0.001 PHE G 268 TRP 0.003 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00441 (13846) covalent geometry : angle 0.54922 (18774) hydrogen bonds : bond 0.03978 ( 769) hydrogen bonds : angle 4.16734 ( 2241) *********************** 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 258 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 0.446 Fit side-chains REVERT: A 74 ARG cc_start: 0.6680 (ttt180) cc_final: 0.6351 (ttp80) REVERT: B 105 LEU cc_start: 0.6446 (mt) cc_final: 0.6177 (mp) REVERT: C 131 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7705 (mtp-110) REVERT: C 134 GLU cc_start: 0.8425 (tt0) cc_final: 0.8160 (tt0) REVERT: C 274 ASP cc_start: 0.9017 (t0) cc_final: 0.8588 (t0) REVERT: D 74 ARG cc_start: 0.6993 (ttt180) cc_final: 0.6343 (ttp80) REVERT: D 115 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8707 (mp) REVERT: D 134 GLU cc_start: 0.8123 (tt0) cc_final: 0.7913 (tt0) REVERT: D 207 ASN cc_start: 0.8546 (m-40) cc_final: 0.8152 (m-40) REVERT: D 210 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8716 (mm110) REVERT: E 74 ARG cc_start: 0.6603 (ttt180) cc_final: 0.6076 (ttp-170) REVERT: E 276 ASN cc_start: 0.8625 (m-40) cc_final: 0.8321 (m110) REVERT: F 56 MET cc_start: 0.7012 (mmt) cc_final: 0.6441 (mmp) REVERT: F 74 ARG cc_start: 0.6742 (ttt180) cc_final: 0.6348 (ttp80) REVERT: G 134 GLU cc_start: 0.8443 (tt0) cc_final: 0.7977 (tt0) outliers start: 31 outliers final: 15 residues processed: 249 average time/residue: 0.1316 time to fit residues: 46.7929 Evaluate side-chains 232 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 216 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 115 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain D residue 64 THR 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 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 8 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 173 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 149 GLN C 149 GLN F 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.149686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.108017 restraints weight = 14525.877| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.46 r_work: 0.2951 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1948 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= 0.107 Angle : 0.468 6.465 18774 Z= 0.257 Chirality : 0.042 0.138 2303 Planarity : 0.004 0.060 2380 Dihedral : 5.148 32.253 1953 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.44 % Allowed : 17.79 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.19), residues: 1778 helix: -0.77 (0.16), residues: 917 sheet: -0.95 (0.27), residues: 294 loop : -1.70 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 74 TYR 0.013 0.001 TYR A 250 PHE 0.028 0.001 PHE D 80 TRP 0.002 0.000 TRP E 251 Details of bonding type rmsd covalent geometry : bond 0.00232 (13846) covalent geometry : angle 0.46793 (18774) hydrogen bonds : bond 0.03466 ( 769) hydrogen bonds : angle 3.80854 ( 2241) *********************** 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 235 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.495 Fit side-chains REVERT: A 74 ARG cc_start: 0.6363 (ttt180) cc_final: 0.6129 (ttp80) REVERT: A 131 ARG cc_start: 0.7937 (mtt180) cc_final: 0.7125 (mtp-110) REVERT: B 272 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8477 (mm-40) REVERT: C 131 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7429 (mtp-110) REVERT: C 134 GLU cc_start: 0.8196 (tt0) cc_final: 0.7765 (tt0) REVERT: D 74 ARG cc_start: 0.6805 (ttt180) cc_final: 0.6166 (ttp80) REVERT: D 115 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8637 (mp) REVERT: D 207 ASN cc_start: 0.8222 (m-40) cc_final: 0.7830 (m-40) REVERT: D 272 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8735 (mm-40) REVERT: E 74 ARG cc_start: 0.6406 (ttt180) cc_final: 0.5931 (ttp80) REVERT: E 276 ASN cc_start: 0.8264 (m-40) cc_final: 0.7683 (m110) REVERT: F 56 MET cc_start: 0.6975 (mmt) cc_final: 0.6431 (mmp) REVERT: F 74 ARG cc_start: 0.6594 (ttt180) cc_final: 0.6192 (ttp80) REVERT: F 273 MET cc_start: 0.8807 (tpp) cc_final: 0.8374 (tpp) REVERT: G 46 ARG cc_start: 0.7540 (mmm-85) cc_final: 0.6890 (mmt90) outliers start: 21 outliers final: 15 residues processed: 226 average time/residue: 0.1232 time to fit residues: 40.1482 Evaluate side-chains 218 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 222 THR 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 273 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 225 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 109 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.150861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.110079 restraints weight = 14383.358| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.39 r_work: 0.2986 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13846 Z= 0.095 Angle : 0.449 8.416 18774 Z= 0.245 Chirality : 0.041 0.139 2303 Planarity : 0.004 0.061 2380 Dihedral : 4.864 31.262 1953 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.13 % Allowed : 18.75 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.20), residues: 1778 helix: -0.21 (0.17), residues: 917 sheet: -0.79 (0.27), residues: 294 loop : -1.48 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 131 TYR 0.012 0.001 TYR G 250 PHE 0.018 0.001 PHE D 80 TRP 0.001 0.000 TRP B 251 Details of bonding type rmsd covalent geometry : bond 0.00200 (13846) covalent geometry : angle 0.44944 (18774) hydrogen bonds : bond 0.03238 ( 769) hydrogen bonds : angle 3.60074 ( 2241) *********************** 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 248 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.488 Fit side-chains REVERT: A 74 ARG cc_start: 0.6524 (ttt180) cc_final: 0.6147 (ttp80) REVERT: A 131 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7177 (mtp-110) REVERT: B 128 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.7974 (mtp-110) REVERT: B 272 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8442 (mm-40) REVERT: B 275 VAL cc_start: 0.9002 (t) cc_final: 0.8788 (p) REVERT: B 276 ASN cc_start: 0.8486 (m-40) cc_final: 0.8081 (m110) REVERT: C 131 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7378 (mtp-110) REVERT: C 134 GLU cc_start: 0.8093 (tt0) cc_final: 0.7425 (tt0) REVERT: D 74 ARG cc_start: 0.6816 (ttt180) cc_final: 0.6221 (ttp80) REVERT: D 115 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8617 (mp) REVERT: D 207 ASN cc_start: 0.8161 (m-40) cc_final: 0.7776 (m-40) REVERT: D 272 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8739 (mm-40) REVERT: E 74 ARG cc_start: 0.6389 (ttt180) cc_final: 0.5880 (ttp80) REVERT: E 276 ASN cc_start: 0.8265 (m-40) cc_final: 0.7693 (m110) REVERT: F 56 MET cc_start: 0.6968 (mmt) cc_final: 0.6425 (mmp) REVERT: F 74 ARG cc_start: 0.6525 (ttt180) cc_final: 0.6282 (ttp80) REVERT: F 272 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8752 (mm-40) REVERT: F 273 MET cc_start: 0.8691 (tpp) cc_final: 0.8407 (ttm) REVERT: G 46 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.6836 (mmt90) REVERT: G 131 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7117 (mtp-110) outliers start: 31 outliers final: 22 residues processed: 239 average time/residue: 0.1214 time to fit residues: 42.3181 Evaluate side-chains 230 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 LEU 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 225 LEU Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 222 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 150 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 149 GLN C 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.146100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.104510 restraints weight = 14646.133| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.47 r_work: 0.2895 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13846 Z= 0.222 Angle : 0.518 5.078 18774 Z= 0.281 Chirality : 0.044 0.148 2303 Planarity : 0.004 0.059 2380 Dihedral : 5.099 31.553 1953 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.27 % Allowed : 19.44 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.20), residues: 1778 helix: -0.17 (0.17), residues: 924 sheet: -0.93 (0.28), residues: 294 loop : -1.35 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 128 TYR 0.013 0.001 TYR A 250 PHE 0.011 0.002 PHE D 80 TRP 0.002 0.001 TRP D 240 Details of bonding type rmsd covalent geometry : bond 0.00537 (13846) covalent geometry : angle 0.51797 (18774) hydrogen bonds : bond 0.03601 ( 769) hydrogen bonds : angle 3.79677 ( 2241) *********************** 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 245 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.462 Fit side-chains REVERT: A 74 ARG cc_start: 0.6478 (ttt180) cc_final: 0.6149 (ttp80) REVERT: A 131 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7371 (mtp-110) REVERT: B 128 ARG cc_start: 0.8371 (mtp-110) cc_final: 0.8170 (mtp-110) REVERT: B 272 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8636 (mm-40) REVERT: C 131 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7536 (mtp-110) REVERT: C 134 GLU cc_start: 0.8356 (tt0) cc_final: 0.7669 (tt0) REVERT: C 272 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8429 (mm-40) REVERT: D 115 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8608 (mp) REVERT: D 134 GLU cc_start: 0.8057 (tt0) cc_final: 0.7705 (tt0) REVERT: D 207 ASN cc_start: 0.8191 (m-40) cc_final: 0.7806 (m-40) REVERT: D 272 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8671 (mm-40) REVERT: E 74 ARG cc_start: 0.6465 (ttt180) cc_final: 0.5893 (ttp-170) REVERT: E 272 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8870 (mm110) REVERT: F 56 MET cc_start: 0.6897 (mmt) cc_final: 0.6322 (mmp) REVERT: F 74 ARG cc_start: 0.6555 (ttt180) cc_final: 0.6299 (ttp80) REVERT: F 134 GLU cc_start: 0.8465 (tt0) cc_final: 0.7940 (tt0) REVERT: G 46 ARG cc_start: 0.7569 (mmm-85) cc_final: 0.6826 (mmt90) REVERT: G 131 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7104 (mtp-110) REVERT: G 134 GLU cc_start: 0.8497 (tt0) cc_final: 0.7855 (tt0) outliers start: 33 outliers final: 25 residues processed: 237 average time/residue: 0.1245 time to fit residues: 42.8361 Evaluate side-chains 231 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 222 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 222 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 73 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 C 149 GLN E 276 ASN G 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.191479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.152052 restraints weight = 13900.738| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.57 r_work: 0.3336 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2400 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= 0.105 Angle : 0.455 8.680 18774 Z= 0.248 Chirality : 0.041 0.137 2303 Planarity : 0.004 0.061 2380 Dihedral : 4.830 30.400 1953 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.13 % Allowed : 19.51 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.20), residues: 1778 helix: 0.08 (0.17), residues: 924 sheet: -0.82 (0.27), residues: 294 loop : -1.21 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 131 TYR 0.013 0.001 TYR A 250 PHE 0.022 0.001 PHE D 80 TRP 0.002 0.000 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00232 (13846) covalent geometry : angle 0.45497 (18774) hydrogen bonds : bond 0.03210 ( 769) hydrogen bonds : angle 3.60400 ( 2241) *********************** 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 242 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.522 Fit side-chains REVERT: A 74 ARG cc_start: 0.6626 (ttt180) cc_final: 0.6311 (ttp80) REVERT: B 56 MET cc_start: 0.7278 (mmp) cc_final: 0.6916 (mmp) REVERT: B 272 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8753 (mm-40) REVERT: C 131 ARG cc_start: 0.8104 (mtt180) cc_final: 0.7738 (mtp-110) REVERT: C 134 GLU cc_start: 0.8024 (tt0) cc_final: 0.7518 (tt0) REVERT: D 115 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8619 (mp) REVERT: D 134 GLU cc_start: 0.7662 (tt0) cc_final: 0.7340 (tt0) REVERT: D 207 ASN cc_start: 0.8318 (m-40) cc_final: 0.7929 (m-40) REVERT: D 272 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8719 (mm-40) REVERT: E 74 ARG cc_start: 0.6518 (ttt180) cc_final: 0.6037 (ttp-170) REVERT: F 56 MET cc_start: 0.6898 (mmt) cc_final: 0.6345 (mmp) REVERT: F 134 GLU cc_start: 0.8172 (tt0) cc_final: 0.7816 (tt0) REVERT: F 277 PHE cc_start: 0.7905 (m-10) cc_final: 0.7658 (m-10) REVERT: G 131 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7377 (mtp-110) REVERT: G 134 GLU cc_start: 0.8240 (tt0) cc_final: 0.7849 (tt0) REVERT: G 274 ASP cc_start: 0.8357 (t0) cc_final: 0.7901 (t0) outliers start: 31 outliers final: 19 residues processed: 235 average time/residue: 0.1306 time to fit residues: 44.2389 Evaluate side-chains 222 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain 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 273 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain 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 61 optimal weight: 0.5980 chunk 114 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 149 GLN C 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.150342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.110344 restraints weight = 14366.510| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.30 r_work: 0.2993 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13846 Z= 0.096 Angle : 0.441 7.353 18774 Z= 0.242 Chirality : 0.041 0.135 2303 Planarity : 0.004 0.059 2380 Dihedral : 4.692 29.734 1953 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.79 % Allowed : 19.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1778 helix: 0.30 (0.17), residues: 924 sheet: -0.74 (0.27), residues: 294 loop : -1.18 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 131 TYR 0.013 0.001 TYR A 250 PHE 0.020 0.001 PHE D 80 TRP 0.001 0.000 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00208 (13846) covalent geometry : angle 0.44103 (18774) hydrogen bonds : bond 0.03125 ( 769) hydrogen bonds : angle 3.57121 ( 2241) *********************** 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 236 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.451 Fit side-chains REVERT: A 74 ARG cc_start: 0.6543 (ttt180) cc_final: 0.6191 (ttp80) REVERT: A 131 ARG cc_start: 0.7669 (mtt90) cc_final: 0.6948 (mtp-110) REVERT: B 272 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8502 (mm-40) REVERT: C 131 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7280 (mtp-110) REVERT: C 134 GLU cc_start: 0.8068 (tt0) cc_final: 0.7250 (tt0) REVERT: C 272 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8387 (mm-40) REVERT: C 273 MET cc_start: 0.8647 (tpp) cc_final: 0.8411 (tpp) REVERT: D 115 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8441 (mp) REVERT: D 134 GLU cc_start: 0.7903 (tt0) cc_final: 0.7411 (tt0) REVERT: D 149 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7959 (mm-40) REVERT: D 207 ASN cc_start: 0.7913 (m-40) cc_final: 0.7559 (m-40) REVERT: D 272 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8625 (mm-40) REVERT: E 74 ARG cc_start: 0.6193 (ttt180) cc_final: 0.5765 (ttp-170) REVERT: E 245 ASP cc_start: 0.8655 (p0) cc_final: 0.8118 (p0) REVERT: E 272 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8440 (mm110) REVERT: F 56 MET cc_start: 0.6587 (mmt) cc_final: 0.6133 (mmp) REVERT: F 134 GLU cc_start: 0.8356 (tt0) cc_final: 0.7704 (tt0) REVERT: G 131 ARG cc_start: 0.7669 (mtt180) cc_final: 0.6754 (mtp-110) REVERT: G 134 GLU cc_start: 0.8349 (tt0) cc_final: 0.7557 (tt0) REVERT: G 274 ASP cc_start: 0.8221 (t0) cc_final: 0.7603 (t0) outliers start: 26 outliers final: 22 residues processed: 228 average time/residue: 0.1182 time to fit residues: 39.6864 Evaluate side-chains 226 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain 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 49 SER Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain 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 30 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 166 optimal weight: 0.0270 chunk 95 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN F 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.151014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.110772 restraints weight = 14361.332| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.29 r_work: 0.3004 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2664 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= 0.096 Angle : 0.443 6.850 18774 Z= 0.241 Chirality : 0.041 0.134 2303 Planarity : 0.004 0.061 2380 Dihedral : 4.600 28.853 1953 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.65 % Allowed : 20.40 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.20), residues: 1778 helix: 0.49 (0.17), residues: 924 sheet: -0.67 (0.28), residues: 294 loop : -1.11 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 131 TYR 0.013 0.001 TYR A 250 PHE 0.017 0.001 PHE D 80 TRP 0.002 0.000 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00210 (13846) covalent geometry : angle 0.44320 (18774) hydrogen bonds : bond 0.03078 ( 769) hydrogen bonds : angle 3.52370 ( 2241) *********************** 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 230 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.514 Fit side-chains REVERT: A 74 ARG cc_start: 0.6542 (ttt180) cc_final: 0.6215 (ttp80) REVERT: A 131 ARG cc_start: 0.7583 (mtt90) cc_final: 0.6906 (mtp-110) REVERT: B 272 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8550 (mm-40) REVERT: C 131 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7298 (mtp-110) REVERT: C 134 GLU cc_start: 0.8085 (tt0) cc_final: 0.7280 (tt0) REVERT: C 272 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8356 (mm-40) REVERT: D 115 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8467 (mp) REVERT: D 134 GLU cc_start: 0.7869 (tt0) cc_final: 0.7389 (tt0) REVERT: D 149 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7930 (mm-40) REVERT: D 207 ASN cc_start: 0.7834 (m-40) cc_final: 0.7448 (m-40) REVERT: D 272 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8761 (mm-40) REVERT: E 74 ARG cc_start: 0.6190 (ttt180) cc_final: 0.5775 (ttp-170) REVERT: E 245 ASP cc_start: 0.8702 (p0) cc_final: 0.8170 (p0) REVERT: F 56 MET cc_start: 0.6519 (mmt) cc_final: 0.6145 (mmp) REVERT: F 134 GLU cc_start: 0.8349 (tt0) cc_final: 0.7741 (tt0) REVERT: F 272 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8708 (mm-40) REVERT: G 131 ARG cc_start: 0.7657 (mtt180) cc_final: 0.6802 (mtp-110) REVERT: G 134 GLU cc_start: 0.8370 (tt0) cc_final: 0.7616 (tt0) REVERT: G 274 ASP cc_start: 0.8262 (t0) cc_final: 0.7675 (t0) outliers start: 24 outliers final: 19 residues processed: 225 average time/residue: 0.1171 time to fit residues: 38.6065 Evaluate side-chains 224 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 105 LEU 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 E residue 49 SER Chi-restraints excluded: chain E residue 222 THR 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 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 33 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 172 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.150844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.109870 restraints weight = 14477.192| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.59 r_work: 0.3155 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2699 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= 0.110 Angle : 0.455 8.127 18774 Z= 0.246 Chirality : 0.041 0.137 2303 Planarity : 0.004 0.060 2380 Dihedral : 4.615 28.869 1953 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.79 % Allowed : 20.05 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1778 helix: 0.59 (0.17), residues: 924 sheet: -0.51 (0.29), residues: 280 loop : -1.07 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 131 TYR 0.013 0.001 TYR A 250 PHE 0.016 0.001 PHE D 80 TRP 0.001 0.000 TRP G 251 Details of bonding type rmsd covalent geometry : bond 0.00248 (13846) covalent geometry : angle 0.45474 (18774) hydrogen bonds : bond 0.03104 ( 769) hydrogen bonds : angle 3.54286 ( 2241) *********************** 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 228 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.477 Fit side-chains REVERT: A 74 ARG cc_start: 0.6824 (ttt180) cc_final: 0.6483 (ttp80) REVERT: A 131 ARG cc_start: 0.7726 (mtt90) cc_final: 0.7352 (mtp-110) REVERT: A 212 GLU cc_start: 0.8783 (tp30) cc_final: 0.8581 (tp30) REVERT: B 272 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8744 (mm-40) REVERT: C 131 ARG cc_start: 0.8026 (mtt180) cc_final: 0.7659 (mtp-110) REVERT: C 134 GLU cc_start: 0.7998 (tt0) cc_final: 0.7502 (tt0) REVERT: D 115 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8600 (mp) REVERT: D 134 GLU cc_start: 0.7608 (tt0) cc_final: 0.7283 (tt0) REVERT: D 207 ASN cc_start: 0.8200 (m-40) cc_final: 0.7811 (m-40) REVERT: D 272 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8148 (mm-40) REVERT: E 74 ARG cc_start: 0.6518 (ttt180) cc_final: 0.6139 (ttp-170) REVERT: E 245 ASP cc_start: 0.8771 (p0) cc_final: 0.8365 (p0) REVERT: E 272 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8429 (mm-40) REVERT: F 56 MET cc_start: 0.6639 (mmt) cc_final: 0.6254 (mmp) REVERT: F 134 GLU cc_start: 0.8120 (tt0) cc_final: 0.7786 (tt0) REVERT: G 131 ARG cc_start: 0.7782 (mtt180) cc_final: 0.7247 (mtp-110) REVERT: G 134 GLU cc_start: 0.8259 (tt0) cc_final: 0.7844 (tt0) REVERT: G 274 ASP cc_start: 0.8294 (t0) cc_final: 0.7894 (t0) outliers start: 26 outliers final: 23 residues processed: 221 average time/residue: 0.1195 time to fit residues: 38.5829 Evaluate side-chains 222 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 105 LEU 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 222 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 222 THR 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 222 THR Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 222 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 65 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.149052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.106894 restraints weight = 14411.094| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.47 r_work: 0.2933 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13846 Z= 0.149 Angle : 0.483 8.074 18774 Z= 0.261 Chirality : 0.042 0.141 2303 Planarity : 0.004 0.061 2380 Dihedral : 4.732 28.828 1953 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.58 % Allowed : 20.12 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.20), residues: 1778 helix: 0.55 (0.17), residues: 924 sheet: -0.54 (0.29), residues: 280 loop : -1.08 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 131 TYR 0.013 0.001 TYR A 250 PHE 0.014 0.001 PHE D 80 TRP 0.002 0.001 TRP B 240 Details of bonding type rmsd covalent geometry : bond 0.00356 (13846) covalent geometry : angle 0.48318 (18774) hydrogen bonds : bond 0.03231 ( 769) hydrogen bonds : angle 3.64886 ( 2241) ********************** 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 228 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.610 Fit side-chains REVERT: A 74 ARG cc_start: 0.6672 (ttt180) cc_final: 0.6310 (ttp80) REVERT: A 131 ARG cc_start: 0.7737 (mtt90) cc_final: 0.7151 (mtp-110) REVERT: B 272 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8615 (mm-40) REVERT: C 131 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7427 (mtp-110) REVERT: C 134 GLU cc_start: 0.8366 (tt0) cc_final: 0.7612 (tt0) REVERT: C 272 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8542 (mm-40) REVERT: D 115 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8552 (mp) REVERT: D 134 GLU cc_start: 0.8037 (tt0) cc_final: 0.7620 (tt0) REVERT: D 149 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8192 (mm-40) REVERT: D 207 ASN cc_start: 0.8081 (m-40) cc_final: 0.7700 (m-40) REVERT: D 272 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8662 (mm-40) REVERT: E 74 ARG cc_start: 0.6444 (ttt180) cc_final: 0.5957 (ttp80) REVERT: E 245 ASP cc_start: 0.8869 (p0) cc_final: 0.8366 (p0) REVERT: F 56 MET cc_start: 0.6748 (mmt) cc_final: 0.6234 (mmp) REVERT: F 134 GLU cc_start: 0.8451 (tt0) cc_final: 0.7929 (tt0) REVERT: G 131 ARG cc_start: 0.7741 (mtt180) cc_final: 0.6994 (mtp-110) REVERT: G 134 GLU cc_start: 0.8499 (tt0) cc_final: 0.7855 (tt0) REVERT: G 274 ASP cc_start: 0.8416 (t0) cc_final: 0.7884 (t0) outliers start: 23 outliers final: 22 residues processed: 223 average time/residue: 0.1134 time to fit residues: 37.1922 Evaluate side-chains 224 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 105 LEU 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 222 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 222 THR 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 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 82 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN C 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.184225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.144512 restraints weight = 13762.702| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.73 r_work: 0.2972 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13846 Z= 0.166 Angle : 0.497 8.082 18774 Z= 0.268 Chirality : 0.043 0.140 2303 Planarity : 0.004 0.060 2380 Dihedral : 4.826 29.757 1953 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.79 % Allowed : 19.99 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1778 helix: 0.51 (0.17), residues: 924 sheet: -0.61 (0.29), residues: 280 loop : -1.11 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 131 TYR 0.014 0.001 TYR A 250 PHE 0.014 0.001 PHE D 80 TRP 0.002 0.001 TRP A 240 Details of bonding type rmsd covalent geometry : bond 0.00395 (13846) covalent geometry : angle 0.49682 (18774) hydrogen bonds : bond 0.03305 ( 769) hydrogen bonds : angle 3.70219 ( 2241) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3143.26 seconds wall clock time: 54 minutes 31.05 seconds (3271.05 seconds total)