Starting phenix.real_space_refine on Fri Jul 3 13:40:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p0o_71089/07_2026/9p0o_71089.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p0o_71089/07_2026/9p0o_71089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p0o_71089/07_2026/9p0o_71089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p0o_71089/07_2026/9p0o_71089.map" model { file = "/net/cci-nas-00/data/ceres_data/9p0o_71089/07_2026/9p0o_71089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p0o_71089/07_2026/9p0o_71089.cif" } resolution = 3.34 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= 0.001 sd= 0.017 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 8995 2.51 5 N 2450 2.21 5 O 2527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14014 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 3.71, per 1000 atoms: 0.26 Number of scatterers: 14014 At special positions: 0 Unit cell: (102.475, 99.9342, 147.361, 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 2527 8.00 N 2450 7.00 C 8995 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: 1.24 Conformation dependent library (CDL) restraints added in 840.0 milliseconds 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 19 sheets defined 54.2% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 21 through 59 removed outlier: 4.278A pdb=" N LEU A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 67 through 90 removed outlier: 3.652A pdb=" N ALA A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 128 removed outlier: 4.584A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASN A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.911A pdb=" N GLY A 140 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.572A pdb=" N ILE A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 167 through 172' Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'B' and resid 20 through 59 removed outlier: 3.639A pdb=" N LEU B 35 " --> pdb=" O ILE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 removed outlier: 3.555A pdb=" N GLY B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 128 removed outlier: 5.230A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN B 117 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 197 through 209 removed outlier: 3.749A pdb=" N ILE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.525A pdb=" N ASP B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 59 Processing helix chain 'C' and resid 68 through 88 removed outlier: 3.871A pdb=" N LEU C 72 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 109 Processing helix chain 'C' and resid 111 through 128 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.979A pdb=" N LYS C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 265 removed outlier: 3.685A pdb=" N TYR C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP C 252 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 60 removed outlier: 3.532A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'D' and resid 68 through 90 removed outlier: 3.537A pdb=" N LEU D 72 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 111 Processing helix chain 'D' and resid 111 through 128 removed outlier: 3.514A pdb=" N LEU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 removed outlier: 3.524A pdb=" N ILE D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 167 through 171' Processing helix chain 'D' and resid 199 through 212 removed outlier: 3.736A pdb=" N ILE D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 265 removed outlier: 3.712A pdb=" N ASP D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 59 removed outlier: 4.111A pdb=" N ALA E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 90 removed outlier: 3.638A pdb=" N ASP E 67 " --> pdb=" O ALA E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 Processing helix chain 'E' and resid 115 through 125 removed outlier: 3.585A pdb=" N ALA E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 197 through 212 removed outlier: 3.528A pdb=" N GLU E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 265 removed outlier: 3.705A pdb=" N GLU E 255 " --> pdb=" O TRP E 251 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG E 256 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 60 removed outlier: 4.337A pdb=" N LEU F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 67 Processing helix chain 'F' and resid 68 through 90 Processing helix chain 'F' and resid 93 through 111 Processing helix chain 'F' and resid 111 through 128 removed outlier: 3.659A pdb=" N ASN F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 172 removed outlier: 3.737A pdb=" N ILE F 170 " --> pdb=" O PRO F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 212 removed outlier: 4.514A pdb=" N GLN F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU F 212 " --> pdb=" O ILE F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 265 removed outlier: 3.725A pdb=" N ARG F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 60 removed outlier: 3.976A pdb=" N ARG G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 67 Processing helix chain 'G' and resid 68 through 90 Processing helix chain 'G' and resid 93 through 128 removed outlier: 4.814A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 172 removed outlier: 3.515A pdb=" N ILE G 170 " --> pdb=" O PRO G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 210 removed outlier: 3.917A pdb=" N GLN G 203 " --> pdb=" O ASP G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 265 removed outlier: 3.673A 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 136 removed outlier: 3.616A pdb=" N VAL A 136 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.516A pdb=" N VAL B 164 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 157 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 136 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 187 removed outlier: 3.641A pdb=" N VAL A 239 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 192 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 187 removed outlier: 3.641A pdb=" N VAL A 239 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 272 through 279 removed outlier: 8.419A pdb=" N MET B 273 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP A 274 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE B 277 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS A 278 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ARG B 279 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL C 275 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL D 275 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N MET E 273 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP D 274 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL E 275 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASN D 276 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE E 277 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N MET F 273 " --> pdb=" O GLN E 272 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASP E 274 " --> pdb=" O MET F 273 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL F 275 " --> pdb=" O ASP E 274 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ASN E 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE F 277 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LYS E 278 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N ARG F 279 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N MET G 273 " --> pdb=" O GLN F 272 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP F 274 " --> pdb=" O MET G 273 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL G 275 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE G 277 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS F 278 " --> pdb=" O PHE G 277 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N MET A 273 " --> pdb=" O ASN G 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.809A pdb=" N ILE C 162 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 136 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 187 removed outlier: 3.611A pdb=" N VAL B 239 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 183 through 187 removed outlier: 3.611A pdb=" N VAL B 239 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 227 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.894A 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: 3.796A pdb=" N ILE D 162 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.751A 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 188 removed outlier: 3.850A pdb=" N VAL C 192 " --> pdb=" O ILE C 233 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 183 through 188 Processing sheet with id=AB3, first strand: chain 'D' and resid 175 through 177 removed outlier: 3.592A pdb=" N ASN D 177 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE E 162 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 165 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E 136 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE E 176 " --> pdb=" O ASP E 137 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 164 " --> pdb=" O ILE E 175 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE F 162 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL F 136 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE F 176 " --> pdb=" O ASP F 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 183 through 188 removed outlier: 3.510A pdb=" N VAL D 239 " --> pdb=" O ASN D 186 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 183 through 185 Processing sheet with id=AB6, first strand: chain 'E' and resid 191 through 192 removed outlier: 3.815A pdb=" N VAL E 192 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 183 through 185 Processing sheet with id=AB8, first strand: chain 'F' and resid 222 through 228 removed outlier: 3.588A pdb=" N ARG F 224 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL F 236 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 135 through 136 Processing sheet with id=AC1, first strand: chain 'G' and resid 183 through 188 removed outlier: 6.413A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N TRP G 240 " --> pdb=" O MET G 221 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N MET G 221 " --> pdb=" O TRP G 240 " (cutoff:3.500A) 883 hydrogen bonds defined for protein. 2565 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: 2.39 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4683 1.34 - 1.46: 2895 1.46 - 1.58: 6527 1.58 - 1.70: 0 1.70 - 1.81: 84 Bond restraints: 14189 Sorted by residual: bond pdb=" CB LYS E 60 " pdb=" CG LYS E 60 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CA ARG D 128 " pdb=" CB ARG D 128 " ideal model delta sigma weight residual 1.522 1.531 -0.009 7.00e-03 2.04e+04 1.51e+00 bond pdb=" CB MET B 56 " pdb=" CG MET B 56 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB ARG G 88 " pdb=" CG ARG G 88 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CA ILE G 162 " pdb=" CB ILE G 162 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.16e+00 ... (remaining 14184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 19112 2.51 - 5.02: 117 5.02 - 7.53: 13 7.53 - 10.05: 6 10.05 - 12.56: 2 Bond angle restraints: 19250 Sorted by residual: angle pdb=" CB MET D 47 " pdb=" CG MET D 47 " pdb=" SD MET D 47 " ideal model delta sigma weight residual 112.70 125.26 -12.56 3.00e+00 1.11e-01 1.75e+01 angle pdb=" CA MET B 56 " pdb=" CB MET B 56 " pdb=" CG MET B 56 " ideal model delta sigma weight residual 114.10 122.05 -7.95 2.00e+00 2.50e-01 1.58e+01 angle pdb=" CB ARG G 88 " pdb=" CG ARG G 88 " pdb=" CD ARG G 88 " ideal model delta sigma weight residual 111.30 119.49 -8.19 2.30e+00 1.89e-01 1.27e+01 angle pdb=" CB LYS E 60 " pdb=" CG LYS E 60 " pdb=" CD LYS E 60 " ideal model delta sigma weight residual 111.30 119.31 -8.01 2.30e+00 1.89e-01 1.21e+01 angle pdb=" CB MET B 56 " pdb=" CG MET B 56 " pdb=" SD MET B 56 " ideal model delta sigma weight residual 112.70 123.00 -10.30 3.00e+00 1.11e-01 1.18e+01 ... (remaining 19245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 7532 16.30 - 32.60: 716 32.60 - 48.90: 221 48.90 - 65.20: 58 65.20 - 81.50: 6 Dihedral angle restraints: 8533 sinusoidal: 3213 harmonic: 5320 Sorted by residual: dihedral pdb=" CA ASP B 218 " pdb=" CB ASP B 218 " pdb=" CG ASP B 218 " pdb=" OD1 ASP B 218 " ideal model delta sinusoidal sigma weight residual -30.00 -89.75 59.75 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CG ARG C 184 " pdb=" CD ARG C 184 " pdb=" NE ARG C 184 " pdb=" CZ ARG C 184 " ideal model delta sinusoidal sigma weight residual -90.00 -133.44 43.44 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" N MET F 126 " pdb=" CA MET F 126 " pdb=" CB MET F 126 " pdb=" CG MET F 126 " ideal model delta sinusoidal sigma weight residual -180.00 -121.13 -58.87 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 8530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2043 0.062 - 0.123: 318 0.123 - 0.185: 10 0.185 - 0.246: 1 0.246 - 0.308: 1 Chirality restraints: 2373 Sorted by residual: chirality pdb=" CG LEU B 42 " pdb=" CB LEU B 42 " pdb=" CD1 LEU B 42 " pdb=" CD2 LEU B 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB VAL A 40 " pdb=" CA VAL A 40 " pdb=" CG1 VAL A 40 " pdb=" CG2 VAL A 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE E 43 " pdb=" CA ILE E 43 " pdb=" CG1 ILE E 43 " pdb=" CG2 ILE E 43 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 2370 not shown) Planarity restraints: 2443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 137 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C ASP C 137 " 0.033 2.00e-02 2.50e+03 pdb=" O ASP C 137 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU C 138 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 153 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C THR G 153 " 0.032 2.00e-02 2.50e+03 pdb=" O THR G 153 " -0.012 2.00e-02 2.50e+03 pdb=" N THR G 154 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP G 218 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" CG ASP G 218 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASP G 218 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP G 218 " -0.008 2.00e-02 2.50e+03 ... (remaining 2440 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 5848 2.93 - 3.42: 14359 3.42 - 3.91: 21713 3.91 - 4.41: 23310 4.41 - 4.90: 40749 Nonbonded interactions: 105979 Sorted by model distance: nonbonded pdb=" O ASP C 137 " pdb=" OD1 ASP C 137 " model vdw 2.437 3.040 nonbonded pdb=" O THR G 93 " pdb=" OG1 THR G 93 " model vdw 2.466 3.040 nonbonded pdb=" O THR A 93 " pdb=" OG1 THR A 93 " model vdw 2.487 3.040 nonbonded pdb=" O THR F 93 " pdb=" OG1 THR F 93 " model vdw 2.506 3.040 nonbonded pdb=" O ASP F 195 " pdb=" OD1 ASP F 195 " model vdw 2.520 3.040 ... (remaining 105974 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: 0.01 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.790 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.003 0.043 14189 Z= 0.147 Angle : 0.558 12.557 19250 Z= 0.301 Chirality : 0.042 0.308 2373 Planarity : 0.003 0.034 2443 Dihedral : 14.752 81.503 5103 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.12 % Allowed : 18.46 % Favored : 79.43 % 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: 0.44 (0.19), residues: 1841 helix: 1.98 (0.17), residues: 919 sheet: -1.28 (0.33), residues: 231 loop : -1.51 (0.21), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 88 TYR 0.019 0.001 TYR F 250 PHE 0.016 0.002 PHE G 277 TRP 0.004 0.001 TRP G 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (14189) covalent geometry : angle 0.55773 / 0.30 (19250) hydrogen bonds : bond 0.15887 / 11.01 ( 871) hydrogen bonds : angle 5.32941 / 3.92 ( 2565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8993 (ttp) cc_final: 0.8770 (ppp) REVERT: A 134 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 56 MET cc_start: 0.7346 (ppp) cc_final: 0.6579 (ppp) REVERT: B 279 ARG cc_start: 0.8632 (ttp-170) cc_final: 0.8244 (tpt170) REVERT: C 188 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: C 278 LYS cc_start: 0.8516 (tttt) cc_final: 0.8115 (ttpp) REVERT: E 273 MET cc_start: 0.8597 (ttm) cc_final: 0.8312 (ttm) REVERT: G 187 GLU cc_start: 0.8445 (pm20) cc_final: 0.7986 (pm20) REVERT: G 198 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6904 (mp) REVERT: G 250 TYR cc_start: 0.8345 (t80) cc_final: 0.8097 (t80) outliers start: 31 outliers final: 26 residues processed: 183 average time/residue: 0.1095 time to fit residues: 30.6020 Evaluate side-chains 184 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 198 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.165510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.128971 restraints weight = 18633.331| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.17 r_work: 0.3489 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.0632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14189 Z= 0.115 Angle : 0.469 7.790 19250 Z= 0.250 Chirality : 0.041 0.140 2373 Planarity : 0.003 0.030 2443 Dihedral : 5.681 59.650 2066 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.67 % Allowed : 18.11 % Favored : 79.22 % 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: 0.80 (0.20), residues: 1841 helix: 2.36 (0.17), residues: 919 sheet: -1.09 (0.33), residues: 232 loop : -1.48 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 88 TYR 0.013 0.001 TYR E 75 PHE 0.015 0.001 PHE B 277 TRP 0.003 0.001 TRP A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (14189) covalent geometry : angle 0.46936 / 0.25 (19250) hydrogen bonds : bond 0.04402 / 3.06 ( 871) hydrogen bonds : angle 3.97318 / 2.92 ( 2565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.9016 (ttp) cc_final: 0.8801 (ppp) REVERT: A 134 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8275 (mt-10) REVERT: B 56 MET cc_start: 0.7564 (ppp) cc_final: 0.6736 (ppp) REVERT: B 279 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.8286 (tpt170) REVERT: C 111 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6230 (pp) REVERT: C 278 LYS cc_start: 0.8508 (tttt) cc_final: 0.8129 (ttpp) REVERT: E 169 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8649 (ttpp) REVERT: E 273 MET cc_start: 0.8633 (ttm) cc_final: 0.8370 (ttm) REVERT: F 195 ASP cc_start: 0.7450 (t0) cc_final: 0.7236 (t0) REVERT: G 198 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6895 (mp) outliers start: 39 outliers final: 22 residues processed: 204 average time/residue: 0.1109 time to fit residues: 34.2585 Evaluate side-chains 181 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 156 optimal weight: 40.0000 chunk 181 optimal weight: 0.0010 chunk 2 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 50 ASN B 149 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.162226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.126411 restraints weight = 19097.560| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.06 r_work: 0.3468 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14189 Z= 0.170 Angle : 0.510 7.786 19250 Z= 0.270 Chirality : 0.042 0.173 2373 Planarity : 0.003 0.035 2443 Dihedral : 4.532 50.336 2032 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.69 % Allowed : 17.77 % Favored : 78.54 % 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: 0.77 (0.20), residues: 1841 helix: 2.35 (0.17), residues: 919 sheet: -1.11 (0.33), residues: 232 loop : -1.52 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 88 TYR 0.012 0.001 TYR C 75 PHE 0.018 0.002 PHE B 277 TRP 0.004 0.001 TRP G 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (14189) covalent geometry : angle 0.50987 / 0.27 (19250) hydrogen bonds : bond 0.04492 / 3.13 ( 871) hydrogen bonds : angle 3.92541 / 2.88 ( 2565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 163 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.9007 (ttp) cc_final: 0.8799 (ppp) REVERT: A 134 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8269 (mt-10) REVERT: B 137 ASP cc_start: 0.8260 (t0) cc_final: 0.8056 (t0) REVERT: B 279 ARG cc_start: 0.8550 (ttp-170) cc_final: 0.8330 (tpt170) REVERT: C 111 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6371 (pp) REVERT: C 278 LYS cc_start: 0.8551 (tttt) cc_final: 0.8313 (ttpp) REVERT: D 56 MET cc_start: 0.8990 (ttp) cc_final: 0.8708 (ttt) REVERT: D 272 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8585 (mm110) REVERT: E 169 LYS cc_start: 0.8947 (ttpp) cc_final: 0.8729 (ttpp) REVERT: E 200 GLN cc_start: 0.7425 (tp-100) cc_final: 0.7123 (tt0) REVERT: E 273 MET cc_start: 0.8594 (ttm) cc_final: 0.8352 (ttm) REVERT: F 68 PHE cc_start: 0.7722 (m-10) cc_final: 0.7490 (m-10) REVERT: G 134 GLU cc_start: 0.7204 (pt0) cc_final: 0.6980 (pt0) REVERT: G 198 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.6964 (mp) outliers start: 54 outliers final: 36 residues processed: 208 average time/residue: 0.0969 time to fit residues: 30.6278 Evaluate side-chains 191 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 206 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 77 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 186 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.159299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.123053 restraints weight = 19055.271| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.14 r_work: 0.3406 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14189 Z= 0.231 Angle : 0.572 9.208 19250 Z= 0.306 Chirality : 0.044 0.150 2373 Planarity : 0.004 0.044 2443 Dihedral : 4.666 48.778 2030 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.72 % Allowed : 17.29 % Favored : 77.99 % 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: 0.58 (0.19), residues: 1841 helix: 2.26 (0.17), residues: 910 sheet: -1.06 (0.33), residues: 224 loop : -1.72 (0.20), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 88 TYR 0.015 0.002 TYR G 194 PHE 0.022 0.002 PHE C 277 TRP 0.006 0.001 TRP G 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.23 (14189) covalent geometry : angle 0.57201 / 0.31 (19250) hydrogen bonds : bond 0.04803 / 3.33 ( 871) hydrogen bonds : angle 4.04140 / 2.96 ( 2565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 157 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.7896 (tt0) cc_final: 0.7643 (tt0) REVERT: A 134 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8435 (mt-10) REVERT: B 279 ARG cc_start: 0.8580 (ttp-170) cc_final: 0.8298 (tpt170) REVERT: C 111 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6416 (pp) REVERT: C 278 LYS cc_start: 0.8604 (tttt) cc_final: 0.8306 (ttmt) REVERT: D 56 MET cc_start: 0.9014 (ttp) cc_final: 0.8766 (ttt) REVERT: E 200 GLN cc_start: 0.7556 (tp-100) cc_final: 0.7282 (tt0) REVERT: E 273 MET cc_start: 0.8663 (ttm) cc_final: 0.8404 (ttm) REVERT: F 254 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7888 (tt) REVERT: G 134 GLU cc_start: 0.7460 (pt0) cc_final: 0.7198 (pt0) REVERT: G 198 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7084 (mp) outliers start: 69 outliers final: 48 residues processed: 213 average time/residue: 0.1017 time to fit residues: 33.0286 Evaluate side-chains 197 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 206 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 41 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 chunk 163 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.163555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.127955 restraints weight = 18837.114| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.04 r_work: 0.3490 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14189 Z= 0.110 Angle : 0.479 7.670 19250 Z= 0.251 Chirality : 0.041 0.210 2373 Planarity : 0.003 0.036 2443 Dihedral : 4.384 46.735 2030 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.03 % Allowed : 18.80 % Favored : 77.17 % 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: 0.84 (0.20), residues: 1841 helix: 2.48 (0.17), residues: 910 sheet: -1.09 (0.32), residues: 238 loop : -1.55 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 88 TYR 0.008 0.001 TYR C 250 PHE 0.013 0.001 PHE B 277 TRP 0.003 0.001 TRP B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14189) covalent geometry : angle 0.47928 / 0.25 (19250) hydrogen bonds : bond 0.03847 / 2.68 ( 871) hydrogen bonds : angle 3.65720 / 2.68 ( 2565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8846 (ppp) cc_final: 0.8505 (ppp) REVERT: A 197 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6720 (m-30) REVERT: A 276 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7146 (p0) REVERT: B 279 ARG cc_start: 0.8520 (ttp-170) cc_final: 0.8259 (tpt170) REVERT: C 111 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6271 (pp) REVERT: C 188 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: C 278 LYS cc_start: 0.8601 (tttt) cc_final: 0.8246 (ttpp) REVERT: D 56 MET cc_start: 0.9001 (ttp) cc_final: 0.8756 (ttt) REVERT: E 200 GLN cc_start: 0.7464 (tp-100) cc_final: 0.7224 (tt0) REVERT: E 273 MET cc_start: 0.8606 (ttm) cc_final: 0.8350 (ttm) REVERT: F 254 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7896 (tt) REVERT: G 56 MET cc_start: 0.8392 (tpt) cc_final: 0.8004 (ttm) REVERT: G 134 GLU cc_start: 0.7229 (pt0) cc_final: 0.6993 (pt0) REVERT: G 198 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6926 (mp) outliers start: 59 outliers final: 40 residues processed: 210 average time/residue: 0.0991 time to fit residues: 31.6624 Evaluate side-chains 200 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 198 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 104 optimal weight: 30.0000 chunk 10 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 103 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.160799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124833 restraints weight = 18953.959| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.12 r_work: 0.3428 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14189 Z= 0.187 Angle : 0.544 13.340 19250 Z= 0.285 Chirality : 0.043 0.173 2373 Planarity : 0.003 0.040 2443 Dihedral : 4.377 46.621 2028 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.90 % Allowed : 19.28 % Favored : 76.83 % 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: 0.72 (0.20), residues: 1841 helix: 2.36 (0.17), residues: 910 sheet: -1.10 (0.33), residues: 238 loop : -1.60 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 224 TYR 0.012 0.001 TYR G 194 PHE 0.018 0.002 PHE B 277 TRP 0.004 0.001 TRP G 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (14189) covalent geometry : angle 0.54425 / 0.28 (19250) hydrogen bonds : bond 0.04309 / 2.99 ( 871) hydrogen bonds : angle 3.80864 / 2.79 ( 2565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 158 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8794 (ppp) cc_final: 0.8467 (ppp) REVERT: A 92 GLN cc_start: 0.7872 (tt0) cc_final: 0.7447 (mt0) REVERT: A 276 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7209 (p0) REVERT: B 279 ARG cc_start: 0.8591 (ttp-170) cc_final: 0.8292 (tpt170) REVERT: C 111 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6452 (pp) REVERT: C 278 LYS cc_start: 0.8616 (tttt) cc_final: 0.8357 (ttpt) REVERT: D 56 MET cc_start: 0.9028 (ttp) cc_final: 0.8815 (ttt) REVERT: E 200 GLN cc_start: 0.7533 (tp-100) cc_final: 0.7301 (tt0) REVERT: E 273 MET cc_start: 0.8672 (ttm) cc_final: 0.8434 (ttm) REVERT: F 254 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7876 (tt) REVERT: G 134 GLU cc_start: 0.7382 (pt0) cc_final: 0.7129 (pt0) REVERT: G 198 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.7067 (mp) outliers start: 57 outliers final: 43 residues processed: 204 average time/residue: 0.1027 time to fit residues: 31.9328 Evaluate side-chains 194 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 206 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 117 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 30.0000 chunk 160 optimal weight: 0.0770 chunk 131 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 145 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.162846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.126417 restraints weight = 18708.804| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.27 r_work: 0.3470 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14189 Z= 0.126 Angle : 0.510 11.077 19250 Z= 0.265 Chirality : 0.042 0.232 2373 Planarity : 0.003 0.038 2443 Dihedral : 4.260 45.684 2028 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.76 % Allowed : 19.75 % Favored : 76.49 % 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: 0.76 (0.20), residues: 1841 helix: 2.43 (0.17), residues: 910 sheet: -1.52 (0.30), residues: 287 loop : -1.37 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 224 TYR 0.012 0.001 TYR C 250 PHE 0.014 0.001 PHE B 277 TRP 0.002 0.001 TRP A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14189) covalent geometry : angle 0.50973 / 0.26 (19250) hydrogen bonds : bond 0.03877 / 2.69 ( 871) hydrogen bonds : angle 3.64790 / 2.68 ( 2565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 155 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8818 (ppp) cc_final: 0.8486 (ppp) REVERT: A 197 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6664 (m-30) REVERT: A 276 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7171 (p0) REVERT: B 148 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7846 (t) REVERT: B 279 ARG cc_start: 0.8574 (ttp-170) cc_final: 0.8249 (tpt170) REVERT: C 111 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6261 (pp) REVERT: C 278 LYS cc_start: 0.8585 (tttt) cc_final: 0.8313 (ttpt) REVERT: D 56 MET cc_start: 0.9015 (ttp) cc_final: 0.8793 (ttt) REVERT: E 273 MET cc_start: 0.8636 (ttm) cc_final: 0.8361 (ttm) REVERT: F 254 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7845 (tt) REVERT: G 56 MET cc_start: 0.8372 (tpt) cc_final: 0.7827 (ttm) REVERT: G 134 GLU cc_start: 0.7302 (pt0) cc_final: 0.7067 (pt0) outliers start: 55 outliers final: 43 residues processed: 200 average time/residue: 0.1054 time to fit residues: 32.3030 Evaluate side-chains 196 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 78 optimal weight: 30.0000 chunk 99 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 180 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 174 ASN ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.162580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.125906 restraints weight = 18756.628| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.09 r_work: 0.3481 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14189 Z= 0.129 Angle : 0.509 10.363 19250 Z= 0.265 Chirality : 0.042 0.211 2373 Planarity : 0.003 0.082 2443 Dihedral : 4.060 41.356 2026 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.21 % Allowed : 20.44 % Favored : 76.35 % 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: 0.80 (0.20), residues: 1841 helix: 2.43 (0.17), residues: 910 sheet: -1.47 (0.30), residues: 287 loop : -1.33 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 88 TYR 0.008 0.001 TYR C 250 PHE 0.015 0.001 PHE B 277 TRP 0.002 0.001 TRP B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14189) covalent geometry : angle 0.50887 / 0.26 (19250) hydrogen bonds : bond 0.03859 / 2.70 ( 871) hydrogen bonds : angle 3.62789 / 2.66 ( 2565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8785 (ppp) cc_final: 0.8458 (ppp) REVERT: A 197 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6663 (m-30) REVERT: B 148 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7810 (t) REVERT: B 279 ARG cc_start: 0.8553 (ttp-170) cc_final: 0.8263 (tpt170) REVERT: C 111 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6391 (pp) REVERT: D 56 MET cc_start: 0.8993 (ttp) cc_final: 0.8772 (ttt) REVERT: E 273 MET cc_start: 0.8619 (ttm) cc_final: 0.8355 (ttm) REVERT: F 254 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7855 (tt) REVERT: G 56 MET cc_start: 0.8369 (tpt) cc_final: 0.8001 (ttm) REVERT: G 134 GLU cc_start: 0.7272 (pt0) cc_final: 0.7045 (pt0) outliers start: 47 outliers final: 39 residues processed: 188 average time/residue: 0.1075 time to fit residues: 30.6945 Evaluate side-chains 191 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 276 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 0 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.160223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.124588 restraints weight = 18875.394| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.23 r_work: 0.3409 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14189 Z= 0.193 Angle : 0.562 11.562 19250 Z= 0.295 Chirality : 0.043 0.254 2373 Planarity : 0.004 0.079 2443 Dihedral : 4.109 42.675 2024 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.62 % Allowed : 20.37 % Favored : 76.01 % 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: 0.63 (0.20), residues: 1841 helix: 2.31 (0.17), residues: 910 sheet: -1.57 (0.30), residues: 287 loop : -1.44 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 88 TYR 0.013 0.001 TYR G 194 PHE 0.018 0.002 PHE B 277 TRP 0.005 0.001 TRP G 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (14189) covalent geometry : angle 0.56225 / 0.30 (19250) hydrogen bonds : bond 0.04301 / 2.98 ( 871) hydrogen bonds : angle 3.79521 / 2.78 ( 2565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 145 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8817 (ppp) cc_final: 0.8496 (ppp) REVERT: A 92 GLN cc_start: 0.7856 (tt0) cc_final: 0.7368 (mt0) REVERT: A 197 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6748 (m-30) REVERT: A 276 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7200 (p0) REVERT: B 126 MET cc_start: 0.7901 (ttp) cc_final: 0.7614 (ttm) REVERT: B 279 ARG cc_start: 0.8552 (ttp-170) cc_final: 0.8228 (tpt170) REVERT: C 111 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6396 (pp) REVERT: C 278 LYS cc_start: 0.8568 (tttt) cc_final: 0.8279 (ttmt) REVERT: D 56 MET cc_start: 0.9001 (ttp) cc_final: 0.8790 (ttt) REVERT: E 273 MET cc_start: 0.8681 (ttm) cc_final: 0.8411 (ttm) REVERT: F 254 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7833 (tt) REVERT: G 56 MET cc_start: 0.8432 (tpt) cc_final: 0.8049 (ttm) REVERT: G 134 GLU cc_start: 0.7440 (pt0) cc_final: 0.7193 (pt0) REVERT: G 187 GLU cc_start: 0.8251 (pm20) cc_final: 0.7919 (pm20) outliers start: 53 outliers final: 45 residues processed: 187 average time/residue: 0.1024 time to fit residues: 29.1781 Evaluate side-chains 192 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 276 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 92 optimal weight: 0.1980 chunk 159 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 168 optimal weight: 0.3980 chunk 169 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 134 optimal weight: 0.0050 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 50 ASN ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.164474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129441 restraints weight = 18762.785| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.13 r_work: 0.3492 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14189 Z= 0.106 Angle : 0.507 12.397 19250 Z= 0.261 Chirality : 0.041 0.244 2373 Planarity : 0.003 0.052 2443 Dihedral : 3.867 42.106 2024 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.21 % Allowed : 20.57 % Favored : 76.21 % 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: 0.91 (0.20), residues: 1841 helix: 2.48 (0.17), residues: 910 sheet: -1.38 (0.31), residues: 273 loop : -1.24 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 88 TYR 0.009 0.001 TYR C 250 PHE 0.012 0.001 PHE B 277 TRP 0.003 0.001 TRP A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (14189) covalent geometry : angle 0.50740 / 0.26 (19250) hydrogen bonds : bond 0.03567 / 2.49 ( 871) hydrogen bonds : angle 3.52772 / 2.59 ( 2565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8788 (ppp) cc_final: 0.8467 (ppp) REVERT: A 197 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6531 (m-30) REVERT: A 276 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7221 (p0) REVERT: B 126 MET cc_start: 0.7828 (ttp) cc_final: 0.7552 (ttm) REVERT: B 148 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7836 (t) REVERT: B 279 ARG cc_start: 0.8520 (ttp-170) cc_final: 0.8251 (tpt170) REVERT: C 111 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6335 (pp) REVERT: C 278 LYS cc_start: 0.8566 (tttt) cc_final: 0.8314 (ttpp) REVERT: D 56 MET cc_start: 0.8984 (ttp) cc_final: 0.8773 (ttt) REVERT: E 273 MET cc_start: 0.8627 (ttm) cc_final: 0.8345 (ttm) REVERT: F 254 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7853 (tt) REVERT: G 56 MET cc_start: 0.8422 (tpt) cc_final: 0.8046 (ttm) REVERT: G 187 GLU cc_start: 0.8176 (pm20) cc_final: 0.7845 (pm20) outliers start: 47 outliers final: 36 residues processed: 191 average time/residue: 0.1071 time to fit residues: 31.3110 Evaluate side-chains 188 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 143 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 45 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.166241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.131241 restraints weight = 18649.042| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.21 r_work: 0.3474 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14189 Z= 0.105 Angle : 0.510 11.842 19250 Z= 0.262 Chirality : 0.041 0.234 2373 Planarity : 0.003 0.037 2443 Dihedral : 3.637 24.057 2021 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.73 % Allowed : 21.60 % Favored : 75.67 % 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: 0.97 (0.20), residues: 1841 helix: 2.52 (0.17), residues: 910 sheet: -1.32 (0.31), residues: 273 loop : -1.21 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 88 TYR 0.014 0.001 TYR C 75 PHE 0.013 0.001 PHE B 277 TRP 0.003 0.000 TRP C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (14189) covalent geometry : angle 0.50991 / 0.26 (19250) hydrogen bonds : bond 0.03441 / 2.40 ( 871) hydrogen bonds : angle 3.45610 / 2.54 ( 2565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3624.65 seconds wall clock time: 62 minutes 36.70 seconds (3756.70 seconds total)