Starting phenix.real_space_refine on Fri Mar 6 06:47:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4e_25673/03_2026/7t4e_25673.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4e_25673/03_2026/7t4e_25673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4e_25673/03_2026/7t4e_25673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4e_25673/03_2026/7t4e_25673.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4e_25673/03_2026/7t4e_25673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4e_25673/03_2026/7t4e_25673.cif" } resolution = 2.87 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= 0.005 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12504 atoms to isotropic. 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 72 5.16 5 C 12216 2.51 5 N 3240 2.21 5 O 3848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19376 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 4.60, per 1000 atoms: 0.24 Number of scatterers: 19376 At special positions: 0 Unit cell: (126.225, 126.225, 129.525, 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 72 16.00 O 3848 8.00 N 3240 7.00 C 12216 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: 1.18 Conformation dependent library (CDL) restraints added in 845.2 milliseconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 34 sheets defined 6.8% alpha, 71.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.757A pdb=" N GLU B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 262 " --> pdb=" O GLY B 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.696A pdb=" N GLU A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 262 " --> pdb=" O GLY A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.759A pdb=" N GLU C 261 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 262 " --> pdb=" O GLY C 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 258 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 320 through 324 Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.698A pdb=" N GLU D 261 " --> pdb=" O LYS D 258 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 262 " --> pdb=" O GLY D 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 258 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 320 through 324 Processing helix chain 'E' and resid 258 through 262 removed outlier: 3.756A pdb=" N GLU E 261 " --> pdb=" O LYS E 258 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL E 262 " --> pdb=" O GLY E 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 258 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 320 through 324 Processing helix chain 'F' and resid 258 through 262 removed outlier: 3.767A pdb=" N GLU F 261 " --> pdb=" O LYS F 258 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 262 " --> pdb=" O GLY F 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 258 through 262' Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 315 through 319 Processing helix chain 'F' and resid 320 through 324 Processing helix chain 'G' and resid 258 through 262 removed outlier: 3.756A pdb=" N GLU G 261 " --> pdb=" O LYS G 258 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL G 262 " --> pdb=" O GLY G 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 258 through 262' Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 315 through 319 Processing helix chain 'G' and resid 320 through 324 Processing helix chain 'H' and resid 258 through 262 removed outlier: 3.820A pdb=" N GLU H 261 " --> pdb=" O LYS H 258 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL H 262 " --> pdb=" O GLY H 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 258 through 262' Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 315 through 319 Processing helix chain 'H' and resid 320 through 324 Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 42 removed outlier: 3.831A pdb=" N GLY B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 49 " --> pdb=" O PHE H 40 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE H 40 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY H 35 " --> pdb=" O GLN H 56 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL H 49 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE G 40 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY G 35 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL G 49 " --> pdb=" O PHE F 40 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE F 40 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY F 35 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL F 49 " --> pdb=" O PHE E 40 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE E 40 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL E 49 " --> pdb=" O PHE D 40 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE D 40 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL D 49 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE C 40 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL C 49 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 40 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL A 49 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE B 40 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 68 removed outlier: 4.275A pdb=" N GLY B 92 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY B 275 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 152 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 277 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 59 through 68 removed outlier: 4.275A pdb=" N GLY B 92 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 106 through 109 removed outlier: 6.241A pdb=" N SER B 125 " --> pdb=" O TRP B 304 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TRP B 304 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLY B 127 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET B 302 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU B 129 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR B 300 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 298 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 203 through 210 removed outlier: 6.395A pdb=" N VAL B 216 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS B 210 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS B 132 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N SER B 125 " --> pdb=" O TRP B 304 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TRP B 304 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLY B 127 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET B 302 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU B 129 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR B 300 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 298 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 172 removed outlier: 7.814A pdb=" N GLU B 160 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ASP B 199 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLU H 160 " --> pdb=" O ASP H 199 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP H 199 " --> pdb=" O GLU H 160 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU G 160 " --> pdb=" O ASP G 199 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASP G 199 " --> pdb=" O GLU G 160 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLU F 160 " --> pdb=" O ASP F 199 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP F 199 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLU E 160 " --> pdb=" O ASP E 199 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ASP E 199 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLU D 160 " --> pdb=" O ASP D 199 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASP D 199 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLU C 160 " --> pdb=" O ASP C 199 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASP C 199 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLU A 160 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ASP A 199 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 59 through 68 removed outlier: 4.188A pdb=" N GLY A 92 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP A 85 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU A 90 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY A 275 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA A 152 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 277 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 59 through 68 removed outlier: 4.188A pdb=" N GLY A 92 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP A 85 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU A 90 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 106 through 109 removed outlier: 6.345A pdb=" N SER A 125 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N TRP A 304 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLY A 127 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET A 302 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU A 129 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR A 300 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP A 298 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 203 through 210 removed outlier: 6.387A pdb=" N VAL A 216 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS A 210 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS A 132 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER A 125 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N TRP A 304 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLY A 127 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET A 302 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU A 129 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR A 300 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP A 298 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 68 removed outlier: 4.256A pdb=" N GLY C 92 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY C 275 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C 152 " --> pdb=" O GLY C 275 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 277 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 68 removed outlier: 4.256A pdb=" N GLY C 92 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 106 through 109 removed outlier: 6.402A pdb=" N SER C 125 " --> pdb=" O TRP C 304 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N TRP C 304 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLY C 127 " --> pdb=" O MET C 302 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET C 302 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU C 129 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR C 300 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP C 298 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 203 through 210 removed outlier: 6.351A pdb=" N VAL C 216 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS C 210 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS C 132 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER C 125 " --> pdb=" O TRP C 304 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N TRP C 304 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLY C 127 " --> pdb=" O MET C 302 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET C 302 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU C 129 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR C 300 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP C 298 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 59 through 68 removed outlier: 4.259A pdb=" N GLY D 92 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY D 275 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA D 152 " --> pdb=" O GLY D 275 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL D 277 " --> pdb=" O ILE D 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 59 through 68 removed outlier: 4.259A pdb=" N GLY D 92 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 106 through 109 removed outlier: 6.373A pdb=" N SER D 125 " --> pdb=" O TRP D 304 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TRP D 304 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLY D 127 " --> pdb=" O MET D 302 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET D 302 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU D 129 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR D 300 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP D 298 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 203 through 210 removed outlier: 6.380A pdb=" N VAL D 216 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS D 210 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LYS D 132 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER D 125 " --> pdb=" O TRP D 304 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TRP D 304 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLY D 127 " --> pdb=" O MET D 302 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET D 302 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU D 129 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR D 300 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP D 298 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 59 through 68 removed outlier: 4.256A pdb=" N GLY E 92 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY E 275 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA E 152 " --> pdb=" O GLY E 275 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL E 277 " --> pdb=" O ILE E 150 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 59 through 68 removed outlier: 4.256A pdb=" N GLY E 92 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 106 through 109 removed outlier: 6.352A pdb=" N SER E 125 " --> pdb=" O TRP E 304 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TRP E 304 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLY E 127 " --> pdb=" O MET E 302 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET E 302 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU E 129 " --> pdb=" O TYR E 300 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR E 300 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP E 298 " --> pdb=" O PRO E 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 203 through 210 removed outlier: 6.425A pdb=" N VAL E 216 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS E 210 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LYS E 132 " --> pdb=" O PHE E 221 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER E 125 " --> pdb=" O TRP E 304 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TRP E 304 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLY E 127 " --> pdb=" O MET E 302 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET E 302 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU E 129 " --> pdb=" O TYR E 300 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR E 300 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP E 298 " --> pdb=" O PRO E 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 59 through 68 removed outlier: 4.279A pdb=" N GLY F 92 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY F 275 " --> pdb=" O ALA F 152 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA F 152 " --> pdb=" O GLY F 275 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL F 277 " --> pdb=" O ILE F 150 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 59 through 68 removed outlier: 4.279A pdb=" N GLY F 92 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 106 through 109 removed outlier: 6.251A pdb=" N SER F 125 " --> pdb=" O TRP F 304 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP F 304 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLY F 127 " --> pdb=" O MET F 302 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET F 302 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU F 129 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR F 300 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP F 298 " --> pdb=" O PRO F 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 203 through 210 removed outlier: 6.373A pdb=" N VAL F 216 " --> pdb=" O ILE F 208 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS F 210 " --> pdb=" O GLU F 214 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LYS F 132 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER F 125 " --> pdb=" O TRP F 304 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP F 304 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLY F 127 " --> pdb=" O MET F 302 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET F 302 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU F 129 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR F 300 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP F 298 " --> pdb=" O PRO F 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 59 through 68 removed outlier: 4.260A pdb=" N GLY G 92 " --> pdb=" O ILE G 83 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY G 275 " --> pdb=" O ALA G 152 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA G 152 " --> pdb=" O GLY G 275 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL G 277 " --> pdb=" O ILE G 150 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 59 through 68 removed outlier: 4.260A pdb=" N GLY G 92 " --> pdb=" O ILE G 83 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 106 through 109 removed outlier: 6.370A pdb=" N SER G 125 " --> pdb=" O TRP G 304 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TRP G 304 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLY G 127 " --> pdb=" O MET G 302 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N MET G 302 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU G 129 " --> pdb=" O TYR G 300 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR G 300 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP G 298 " --> pdb=" O PRO G 131 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 203 through 210 removed outlier: 6.362A pdb=" N VAL G 216 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS G 210 " --> pdb=" O GLU G 214 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU G 214 " --> pdb=" O LYS G 210 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LYS G 132 " --> pdb=" O PHE G 221 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER G 125 " --> pdb=" O TRP G 304 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TRP G 304 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLY G 127 " --> pdb=" O MET G 302 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N MET G 302 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU G 129 " --> pdb=" O TYR G 300 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR G 300 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP G 298 " --> pdb=" O PRO G 131 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 59 through 68 removed outlier: 4.221A pdb=" N GLY H 92 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY H 275 " --> pdb=" O ALA H 152 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA H 152 " --> pdb=" O GLY H 275 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL H 277 " --> pdb=" O ILE H 150 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 59 through 68 removed outlier: 4.221A pdb=" N GLY H 92 " --> pdb=" O ILE H 83 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 106 through 109 removed outlier: 6.250A pdb=" N SER H 125 " --> pdb=" O TRP H 304 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP H 304 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLY H 127 " --> pdb=" O MET H 302 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N MET H 302 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU H 129 " --> pdb=" O TYR H 300 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR H 300 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP H 298 " --> pdb=" O PRO H 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 203 through 210 removed outlier: 6.339A pdb=" N VAL H 216 " --> pdb=" O ILE H 208 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS H 210 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU H 214 " --> pdb=" O LYS H 210 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LYS H 132 " --> pdb=" O PHE H 221 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER H 125 " --> pdb=" O TRP H 304 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP H 304 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLY H 127 " --> pdb=" O MET H 302 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N MET H 302 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU H 129 " --> pdb=" O TYR H 300 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR H 300 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP H 298 " --> pdb=" O PRO H 131 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3267 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: 3.73 Time building geometry restraints manager: 1.61 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: 6296 1.34 - 1.46: 4114 1.46 - 1.57: 9222 1.57 - 1.69: 0 1.69 - 1.80: 144 Bond restraints: 19776 Sorted by residual: bond pdb=" N SER B 174 " pdb=" CA SER B 174 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.35e+00 bond pdb=" N SER C 174 " pdb=" CA SER C 174 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.27e+00 bond pdb=" CA THR G 70 " pdb=" C THR G 70 " ideal model delta sigma weight residual 1.519 1.529 -0.010 9.50e-03 1.11e+04 1.10e+00 bond pdb=" CG1 ILE E 167 " pdb=" CD1 ILE E 167 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.05e+00 bond pdb=" CG1 ILE D 301 " pdb=" CD1 ILE D 301 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.02e+00 ... (remaining 19771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 26489 1.79 - 3.57: 280 3.57 - 5.36: 28 5.36 - 7.15: 8 7.15 - 8.93: 3 Bond angle restraints: 26808 Sorted by residual: angle pdb=" C TRP H 233 " pdb=" N ASN H 234 " pdb=" CA ASN H 234 " ideal model delta sigma weight residual 121.61 129.71 -8.10 1.39e+00 5.18e-01 3.40e+01 angle pdb=" C TRP A 233 " pdb=" N ASN A 234 " pdb=" CA ASN A 234 " ideal model delta sigma weight residual 121.83 130.76 -8.93 1.56e+00 4.11e-01 3.28e+01 angle pdb=" C SER C 174 " pdb=" CA SER C 174 " pdb=" CB SER C 174 " ideal model delta sigma weight residual 110.42 115.75 -5.33 1.99e+00 2.53e-01 7.18e+00 angle pdb=" C SER B 174 " pdb=" CA SER B 174 " pdb=" CB SER B 174 " ideal model delta sigma weight residual 110.42 115.68 -5.26 1.99e+00 2.53e-01 7.00e+00 angle pdb=" CA TYR E 192 " pdb=" CB TYR E 192 " pdb=" CG TYR E 192 " ideal model delta sigma weight residual 113.90 117.65 -3.75 1.80e+00 3.09e-01 4.33e+00 ... (remaining 26803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 10907 16.94 - 33.87: 788 33.87 - 50.81: 107 50.81 - 67.75: 32 67.75 - 84.69: 38 Dihedral angle restraints: 11872 sinusoidal: 4768 harmonic: 7104 Sorted by residual: dihedral pdb=" CA LYS G 132 " pdb=" C LYS G 132 " pdb=" N LYS G 133 " pdb=" CA LYS G 133 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LYS C 132 " pdb=" C LYS C 132 " pdb=" N LYS C 133 " pdb=" CA LYS C 133 " ideal model delta harmonic sigma weight residual 180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ASN A 140 " pdb=" CB ASN A 140 " pdb=" CG ASN A 140 " pdb=" OD1 ASN A 140 " ideal model delta sinusoidal sigma weight residual 120.00 -172.62 -67.38 2 2.00e+01 2.50e-03 1.02e+01 ... (remaining 11869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1702 0.031 - 0.061: 792 0.061 - 0.092: 195 0.092 - 0.122: 202 0.122 - 0.153: 45 Chirality restraints: 2936 Sorted by residual: chirality pdb=" CA TYR E 192 " pdb=" N TYR E 192 " pdb=" C TYR E 192 " pdb=" CB TYR E 192 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE H 301 " pdb=" N ILE H 301 " pdb=" C ILE H 301 " pdb=" CB ILE H 301 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ILE B 301 " pdb=" N ILE B 301 " pdb=" C ILE B 301 " pdb=" CB ILE B 301 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 2933 not shown) Planarity restraints: 3464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 118 " -0.049 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO D 119 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN H 118 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO H 119 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO H 119 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 119 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 118 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A 119 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.040 5.00e-02 4.00e+02 ... (remaining 3461 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 312 2.67 - 3.23: 17128 3.23 - 3.79: 29840 3.79 - 4.34: 43004 4.34 - 4.90: 71346 Nonbonded interactions: 161630 Sorted by model distance: nonbonded pdb=" OG SER A 280 " pdb=" OG1 THR A 284 " model vdw 2.117 3.040 nonbonded pdb=" OH TYR G 237 " pdb=" OH TYR G 247 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR C 237 " pdb=" OH TYR C 247 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR D 237 " pdb=" OH TYR D 247 " model vdw 2.188 3.040 nonbonded pdb=" OG SER F 280 " pdb=" OG1 THR F 284 " model vdw 2.199 3.040 ... (remaining 161625 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' selection = chain 'H' } 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.940 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 : 0.002 0.040 19776 Z= 0.120 Angle : 0.525 8.932 26808 Z= 0.295 Chirality : 0.046 0.153 2936 Planarity : 0.006 0.074 3464 Dihedral : 12.915 84.687 7344 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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 (0.17), residues: 2424 helix: -2.80 (0.41), residues: 96 sheet: 0.39 (0.14), residues: 1400 loop : -1.38 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 225 TYR 0.016 0.001 TYR G 237 PHE 0.011 0.001 PHE F 100 TRP 0.019 0.001 TRP A 217 Details of bonding type rmsd covalent geometry : bond 0.00236 (19776) covalent geometry : angle 0.52513 (26808) hydrogen bonds : bond 0.13833 ( 936) hydrogen bonds : angle 7.01634 ( 3267) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 829 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 ILE cc_start: 0.7926 (mm) cc_final: 0.7694 (mp) REVERT: B 69 ASP cc_start: 0.6736 (m-30) cc_final: 0.6470 (m-30) REVERT: B 72 ASN cc_start: 0.8115 (m110) cc_final: 0.7829 (m110) REVERT: B 135 ARG cc_start: 0.7619 (tpp80) cc_final: 0.7333 (tpp80) REVERT: B 160 GLU cc_start: 0.7197 (pm20) cc_final: 0.6988 (pm20) REVERT: B 202 ASP cc_start: 0.7115 (m-30) cc_final: 0.6797 (m-30) REVERT: B 231 ASN cc_start: 0.7949 (m110) cc_final: 0.7681 (m-40) REVERT: B 237 TYR cc_start: 0.8205 (m-80) cc_final: 0.7894 (m-80) REVERT: B 294 SER cc_start: 0.8296 (t) cc_final: 0.7866 (m) REVERT: B 308 GLU cc_start: 0.6952 (pm20) cc_final: 0.6579 (pm20) REVERT: A 133 LYS cc_start: 0.8145 (tttm) cc_final: 0.7717 (tttm) REVERT: A 165 ASP cc_start: 0.6764 (m-30) cc_final: 0.6552 (m-30) REVERT: A 226 ASP cc_start: 0.6877 (t0) cc_final: 0.6538 (t0) REVERT: A 237 TYR cc_start: 0.8342 (m-80) cc_final: 0.8113 (m-10) REVERT: A 246 ARG cc_start: 0.7521 (tpp80) cc_final: 0.7165 (tpp80) REVERT: A 258 LYS cc_start: 0.8814 (ptpp) cc_final: 0.8580 (ptpp) REVERT: A 296 MET cc_start: 0.7604 (mpp) cc_final: 0.6963 (mpp) REVERT: A 308 GLU cc_start: 0.7075 (pm20) cc_final: 0.6761 (pm20) REVERT: A 329 GLU cc_start: 0.6535 (mt-10) cc_final: 0.5990 (mt-10) REVERT: C 72 ASN cc_start: 0.7928 (m-40) cc_final: 0.7657 (m110) REVERT: C 202 ASP cc_start: 0.7134 (m-30) cc_final: 0.6844 (m-30) REVERT: C 218 ASP cc_start: 0.6708 (m-30) cc_final: 0.6328 (m-30) REVERT: C 308 GLU cc_start: 0.7001 (pm20) cc_final: 0.6606 (pm20) REVERT: D 36 THR cc_start: 0.8234 (p) cc_final: 0.8025 (m) REVERT: D 112 LYS cc_start: 0.7774 (mttp) cc_final: 0.7530 (mttt) REVERT: D 133 LYS cc_start: 0.8169 (tttm) cc_final: 0.7519 (tttm) REVERT: D 258 LYS cc_start: 0.8734 (ptpp) cc_final: 0.8530 (ptpp) REVERT: D 296 MET cc_start: 0.7155 (mpp) cc_final: 0.6573 (mpp) REVERT: D 308 GLU cc_start: 0.6905 (pm20) cc_final: 0.6541 (pm20) REVERT: E 33 VAL cc_start: 0.8593 (p) cc_final: 0.8254 (t) REVERT: E 61 ILE cc_start: 0.8005 (mm) cc_final: 0.7787 (mp) REVERT: E 69 ASP cc_start: 0.6734 (m-30) cc_final: 0.6439 (m-30) REVERT: E 133 LYS cc_start: 0.8320 (tttm) cc_final: 0.7989 (tttp) REVERT: E 143 ILE cc_start: 0.8504 (mm) cc_final: 0.8259 (mt) REVERT: E 202 ASP cc_start: 0.7023 (m-30) cc_final: 0.6810 (m-30) REVERT: E 308 GLU cc_start: 0.7106 (pm20) cc_final: 0.6785 (pm20) REVERT: F 48 ILE cc_start: 0.8415 (mt) cc_final: 0.8187 (pp) REVERT: F 159 LYS cc_start: 0.7924 (pttm) cc_final: 0.7610 (pttm) REVERT: F 294 SER cc_start: 0.8103 (m) cc_final: 0.7890 (t) REVERT: F 308 GLU cc_start: 0.6834 (pm20) cc_final: 0.6415 (pm20) REVERT: F 329 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6150 (mt-10) REVERT: G 33 VAL cc_start: 0.8559 (p) cc_final: 0.8279 (t) REVERT: G 308 GLU cc_start: 0.7078 (pm20) cc_final: 0.6808 (pm20) REVERT: H 48 ILE cc_start: 0.8433 (mt) cc_final: 0.8219 (pp) REVERT: H 58 ARG cc_start: 0.8753 (ttt180) cc_final: 0.8549 (ttt180) REVERT: H 63 ASN cc_start: 0.7642 (t0) cc_final: 0.7432 (t0) REVERT: H 96 SER cc_start: 0.8347 (m) cc_final: 0.8143 (m) REVERT: H 165 ASP cc_start: 0.6676 (m-30) cc_final: 0.6454 (m-30) REVERT: H 258 LYS cc_start: 0.8688 (ptpp) cc_final: 0.8457 (ptpp) REVERT: H 296 MET cc_start: 0.7475 (mpp) cc_final: 0.7084 (mpp) REVERT: H 308 GLU cc_start: 0.6961 (pm20) cc_final: 0.6561 (pm20) REVERT: H 329 GLU cc_start: 0.6190 (mt-10) cc_final: 0.5971 (mt-10) outliers start: 0 outliers final: 0 residues processed: 829 average time/residue: 0.7384 time to fit residues: 673.9808 Evaluate side-chains 781 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 781 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.0370 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN D 231 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN F 155 ASN F 207 GLN ** G 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 ASN H 155 ASN H 207 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.116607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.107000 restraints weight = 27893.264| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.97 r_work: 0.3319 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19776 Z= 0.197 Angle : 0.547 9.055 26808 Z= 0.296 Chirality : 0.048 0.161 2936 Planarity : 0.006 0.048 3464 Dihedral : 4.519 16.856 2672 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.67 % Allowed : 12.92 % Favored : 85.42 % 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: -0.75 (0.17), residues: 2424 helix: -2.52 (0.42), residues: 96 sheet: 0.18 (0.14), residues: 1400 loop : -1.24 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 135 TYR 0.029 0.001 TYR G 237 PHE 0.010 0.001 PHE F 100 TRP 0.007 0.001 TRP A 217 Details of bonding type rmsd covalent geometry : bond 0.00422 (19776) covalent geometry : angle 0.54669 (26808) hydrogen bonds : bond 0.03634 ( 936) hydrogen bonds : angle 5.14693 ( 3267) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 799 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: B 49 VAL cc_start: 0.9034 (m) cc_final: 0.8777 (p) REVERT: B 63 ASN cc_start: 0.8368 (t0) cc_final: 0.8094 (t0) REVERT: B 69 ASP cc_start: 0.7711 (m-30) cc_final: 0.7485 (m-30) REVERT: B 72 ASN cc_start: 0.8452 (m110) cc_final: 0.7976 (m110) REVERT: B 107 TYR cc_start: 0.8458 (m-80) cc_final: 0.8152 (m-80) REVERT: B 133 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8448 (ttmm) REVERT: B 160 GLU cc_start: 0.8124 (pm20) cc_final: 0.7817 (pm20) REVERT: B 164 SER cc_start: 0.8465 (t) cc_final: 0.8154 (p) REVERT: B 202 ASP cc_start: 0.7860 (m-30) cc_final: 0.7500 (m-30) REVERT: B 237 TYR cc_start: 0.8540 (m-80) cc_final: 0.8334 (m-80) REVERT: B 308 GLU cc_start: 0.7593 (pm20) cc_final: 0.7212 (pm20) REVERT: A 226 ASP cc_start: 0.7700 (t0) cc_final: 0.7271 (t0) REVERT: A 239 ASN cc_start: 0.7962 (t0) cc_final: 0.7699 (t0) REVERT: A 244 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7343 (ttp-170) REVERT: A 246 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7621 (tpp80) REVERT: A 258 LYS cc_start: 0.8969 (ptpp) cc_final: 0.8599 (ptpp) REVERT: A 299 MET cc_start: 0.8361 (tpp) cc_final: 0.8109 (mmt) REVERT: A 308 GLU cc_start: 0.7738 (pm20) cc_final: 0.7424 (pm20) REVERT: A 321 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7812 (mmmt) REVERT: C 33 VAL cc_start: 0.8646 (p) cc_final: 0.8351 (t) REVERT: C 63 ASN cc_start: 0.8269 (t0) cc_final: 0.7958 (t0) REVERT: C 66 ASP cc_start: 0.8102 (t0) cc_final: 0.7851 (t0) REVERT: C 72 ASN cc_start: 0.8321 (m-40) cc_final: 0.7831 (m110) REVERT: C 202 ASP cc_start: 0.7806 (m-30) cc_final: 0.7473 (m-30) REVERT: C 246 ARG cc_start: 0.7598 (tpp80) cc_final: 0.7270 (tpp80) REVERT: C 255 ASN cc_start: 0.8485 (t0) cc_final: 0.8147 (t0) REVERT: C 295 ARG cc_start: 0.8708 (ttp80) cc_final: 0.8496 (ttm170) REVERT: C 302 MET cc_start: 0.8430 (tpp) cc_final: 0.8212 (tpp) REVERT: C 308 GLU cc_start: 0.7732 (pm20) cc_final: 0.7308 (pm20) REVERT: D 41 GLU cc_start: 0.7959 (tt0) cc_final: 0.7724 (tt0) REVERT: D 112 LYS cc_start: 0.7791 (mttp) cc_final: 0.7461 (mttt) REVERT: D 255 ASN cc_start: 0.8451 (t0) cc_final: 0.8225 (t0) REVERT: D 258 LYS cc_start: 0.8906 (ptpp) cc_final: 0.8640 (ptpp) REVERT: D 308 GLU cc_start: 0.7681 (pm20) cc_final: 0.7273 (pm20) REVERT: E 41 GLU cc_start: 0.7915 (tt0) cc_final: 0.7612 (tt0) REVERT: E 69 ASP cc_start: 0.7671 (m-30) cc_final: 0.7438 (m-30) REVERT: E 133 LYS cc_start: 0.8653 (tttm) cc_final: 0.8297 (tttm) REVERT: E 135 ARG cc_start: 0.8296 (tpp80) cc_final: 0.7904 (tpp-160) REVERT: E 137 GLU cc_start: 0.7621 (mp0) cc_final: 0.7262 (mp0) REVERT: E 169 TYR cc_start: 0.7554 (m-80) cc_final: 0.7353 (m-10) REVERT: E 202 ASP cc_start: 0.7757 (m-30) cc_final: 0.7498 (m-30) REVERT: E 255 ASN cc_start: 0.8500 (t0) cc_final: 0.8172 (t0) REVERT: E 308 GLU cc_start: 0.7801 (pm20) cc_final: 0.7452 (pm20) REVERT: F 48 ILE cc_start: 0.8530 (mt) cc_final: 0.8267 (pp) REVERT: F 63 ASN cc_start: 0.8261 (t0) cc_final: 0.7949 (t0) REVERT: F 69 ASP cc_start: 0.7580 (m-30) cc_final: 0.7329 (m-30) REVERT: F 132 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8381 (ttpt) REVERT: F 137 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7859 (mt-10) REVERT: F 308 GLU cc_start: 0.7630 (pm20) cc_final: 0.7195 (pm20) REVERT: G 33 VAL cc_start: 0.8638 (p) cc_final: 0.8353 (t) REVERT: G 37 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7471 (mt-10) REVERT: G 63 ASN cc_start: 0.8298 (t0) cc_final: 0.8064 (t0) REVERT: G 137 GLU cc_start: 0.7766 (mp0) cc_final: 0.7264 (mp0) REVERT: G 208 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8516 (pt) REVERT: G 241 MET cc_start: 0.8087 (mtm) cc_final: 0.7854 (mtp) REVERT: G 308 GLU cc_start: 0.7695 (pm20) cc_final: 0.7282 (pm20) REVERT: G 329 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6847 (mt-10) REVERT: H 50 LYS cc_start: 0.8287 (tttp) cc_final: 0.8006 (ttmm) REVERT: H 258 LYS cc_start: 0.8924 (ptpp) cc_final: 0.8595 (ptpp) REVERT: H 308 GLU cc_start: 0.7642 (pm20) cc_final: 0.7211 (pm20) outliers start: 36 outliers final: 12 residues processed: 806 average time/residue: 0.7666 time to fit residues: 677.0746 Evaluate side-chains 790 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 775 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 322 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 144 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN C 231 ASN C 316 ASN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106659 restraints weight = 27980.290| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.97 r_work: 0.3310 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19776 Z= 0.187 Angle : 0.536 8.822 26808 Z= 0.289 Chirality : 0.047 0.154 2936 Planarity : 0.005 0.058 3464 Dihedral : 4.480 16.267 2672 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.94 % Allowed : 15.46 % Favored : 82.59 % 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: -0.85 (0.17), residues: 2424 helix: -2.39 (0.44), residues: 96 sheet: 0.12 (0.14), residues: 1400 loop : -1.34 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 106 TYR 0.023 0.001 TYR G 237 PHE 0.013 0.001 PHE F 242 TRP 0.007 0.001 TRP A 217 Details of bonding type rmsd covalent geometry : bond 0.00401 (19776) covalent geometry : angle 0.53593 (26808) hydrogen bonds : bond 0.03421 ( 936) hydrogen bonds : angle 4.99421 ( 3267) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 796 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: B 49 VAL cc_start: 0.9031 (m) cc_final: 0.8793 (p) REVERT: B 69 ASP cc_start: 0.7723 (m-30) cc_final: 0.7465 (m-30) REVERT: B 75 SER cc_start: 0.8704 (t) cc_final: 0.8402 (p) REVERT: B 86 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8562 (mmtp) REVERT: B 108 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8486 (m) REVERT: B 132 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8280 (ttpt) REVERT: B 133 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8301 (ttmm) REVERT: B 160 GLU cc_start: 0.8148 (pm20) cc_final: 0.7770 (pm20) REVERT: B 202 ASP cc_start: 0.7851 (m-30) cc_final: 0.7456 (m-30) REVERT: B 237 TYR cc_start: 0.8646 (m-80) cc_final: 0.8410 (m-10) REVERT: B 308 GLU cc_start: 0.7629 (pm20) cc_final: 0.7226 (pm20) REVERT: A 226 ASP cc_start: 0.7714 (t0) cc_final: 0.7343 (t70) REVERT: A 244 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7458 (ttp-170) REVERT: A 246 ARG cc_start: 0.8140 (tpp80) cc_final: 0.7762 (tpp80) REVERT: A 258 LYS cc_start: 0.8939 (ptpp) cc_final: 0.8609 (ptpp) REVERT: A 274 MET cc_start: 0.8245 (mtp) cc_final: 0.7976 (mtp) REVERT: A 299 MET cc_start: 0.8365 (tpp) cc_final: 0.8083 (mmt) REVERT: A 308 GLU cc_start: 0.7721 (pm20) cc_final: 0.7409 (pm20) REVERT: A 321 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7769 (mmmt) REVERT: A 340 ARG cc_start: 0.8788 (mtm-85) cc_final: 0.8579 (mtm-85) REVERT: C 33 VAL cc_start: 0.8661 (p) cc_final: 0.8363 (t) REVERT: C 62 TYR cc_start: 0.8525 (m-80) cc_final: 0.8066 (m-80) REVERT: C 63 ASN cc_start: 0.8285 (t0) cc_final: 0.7947 (t0) REVERT: C 72 ASN cc_start: 0.8306 (m-40) cc_final: 0.7623 (m110) REVERT: C 86 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8613 (mmtp) REVERT: C 187 GLU cc_start: 0.7029 (tp30) cc_final: 0.6670 (mp0) REVERT: C 202 ASP cc_start: 0.7772 (m-30) cc_final: 0.7434 (m-30) REVERT: C 296 MET cc_start: 0.8194 (mpp) cc_final: 0.7766 (mpp) REVERT: C 302 MET cc_start: 0.8473 (tpp) cc_final: 0.8242 (tpp) REVERT: C 308 GLU cc_start: 0.7749 (pm20) cc_final: 0.7324 (pm20) REVERT: C 322 GLU cc_start: 0.8371 (pt0) cc_final: 0.8100 (pt0) REVERT: D 41 GLU cc_start: 0.7964 (tt0) cc_final: 0.7734 (tt0) REVERT: D 132 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8158 (ttpt) REVERT: D 258 LYS cc_start: 0.8895 (ptpp) cc_final: 0.8643 (ptpp) REVERT: D 308 GLU cc_start: 0.7650 (pm20) cc_final: 0.7252 (pm20) REVERT: E 41 GLU cc_start: 0.7897 (tt0) cc_final: 0.7542 (tt0) REVERT: E 69 ASP cc_start: 0.7675 (m-30) cc_final: 0.7443 (m-30) REVERT: E 133 LYS cc_start: 0.8657 (tttm) cc_final: 0.8175 (tttm) REVERT: E 135 ARG cc_start: 0.8368 (tpp80) cc_final: 0.8055 (tpp80) REVERT: E 137 GLU cc_start: 0.7659 (mp0) cc_final: 0.7277 (mp0) REVERT: E 169 TYR cc_start: 0.7545 (m-80) cc_final: 0.7327 (m-10) REVERT: E 202 ASP cc_start: 0.7793 (m-30) cc_final: 0.7461 (m-30) REVERT: E 258 LYS cc_start: 0.9020 (ptpp) cc_final: 0.8765 (ptpp) REVERT: E 296 MET cc_start: 0.8310 (mpp) cc_final: 0.7736 (mpp) REVERT: E 308 GLU cc_start: 0.7801 (pm20) cc_final: 0.7435 (pm20) REVERT: F 48 ILE cc_start: 0.8545 (mt) cc_final: 0.8274 (pp) REVERT: F 63 ASN cc_start: 0.8207 (t0) cc_final: 0.7990 (t0) REVERT: F 69 ASP cc_start: 0.7537 (m-30) cc_final: 0.7296 (m-30) REVERT: F 137 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7885 (mt-10) REVERT: F 308 GLU cc_start: 0.7643 (pm20) cc_final: 0.7233 (pm20) REVERT: G 33 VAL cc_start: 0.8665 (p) cc_final: 0.8373 (t) REVERT: G 37 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7428 (mt-10) REVERT: G 63 ASN cc_start: 0.8302 (t0) cc_final: 0.8028 (t0) REVERT: G 70 THR cc_start: 0.8301 (p) cc_final: 0.8063 (p) REVERT: G 133 LYS cc_start: 0.8740 (tttm) cc_final: 0.8128 (tttm) REVERT: G 137 GLU cc_start: 0.7756 (mp0) cc_final: 0.7284 (mp0) REVERT: G 296 MET cc_start: 0.8295 (mpp) cc_final: 0.7558 (mpp) REVERT: G 308 GLU cc_start: 0.7665 (pm20) cc_final: 0.7232 (pm20) REVERT: G 329 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6787 (mt-10) REVERT: H 50 LYS cc_start: 0.8304 (tttp) cc_final: 0.8003 (ttmm) REVERT: H 63 ASN cc_start: 0.8236 (t0) cc_final: 0.7906 (t0) REVERT: H 132 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8441 (ttpt) REVERT: H 159 LYS cc_start: 0.8487 (pttm) cc_final: 0.7919 (pttm) REVERT: H 258 LYS cc_start: 0.8931 (ptpp) cc_final: 0.8585 (ptpp) REVERT: H 308 GLU cc_start: 0.7642 (pm20) cc_final: 0.7268 (pm20) outliers start: 42 outliers final: 16 residues processed: 804 average time/residue: 0.7750 time to fit residues: 682.7537 Evaluate side-chains 794 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 772 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 169 TYR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 236 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 221 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 218 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN B 72 ASN B 316 ASN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN D 98 ASN F 98 ASN H 98 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.103544 restraints weight = 28057.332| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.93 r_work: 0.3263 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 19776 Z= 0.384 Angle : 0.627 8.390 26808 Z= 0.339 Chirality : 0.050 0.171 2936 Planarity : 0.006 0.065 3464 Dihedral : 5.020 23.613 2672 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.87 % Allowed : 17.64 % Favored : 79.49 % 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: -0.83 (0.17), residues: 2424 helix: -4.11 (0.23), residues: 48 sheet: 0.14 (0.14), residues: 1360 loop : -1.27 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 135 TYR 0.037 0.002 TYR G 237 PHE 0.012 0.002 PHE B 333 TRP 0.013 0.002 TRP B 130 Details of bonding type rmsd covalent geometry : bond 0.00830 (19776) covalent geometry : angle 0.62722 (26808) hydrogen bonds : bond 0.03856 ( 936) hydrogen bonds : angle 5.14945 ( 3267) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 785 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: B 62 TYR cc_start: 0.8713 (m-80) cc_final: 0.8033 (m-80) REVERT: B 69 ASP cc_start: 0.7703 (m-30) cc_final: 0.7491 (m-30) REVERT: B 202 ASP cc_start: 0.7892 (m-30) cc_final: 0.7494 (m-30) REVERT: B 237 TYR cc_start: 0.8700 (m-80) cc_final: 0.8466 (m-10) REVERT: B 258 LYS cc_start: 0.8943 (ptpp) cc_final: 0.8727 (ptpp) REVERT: B 308 GLU cc_start: 0.7716 (pm20) cc_final: 0.7227 (pm20) REVERT: A 135 ARG cc_start: 0.8500 (tpp80) cc_final: 0.8102 (tpp-160) REVERT: A 226 ASP cc_start: 0.7837 (t0) cc_final: 0.7377 (t0) REVERT: A 246 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7798 (mpp80) REVERT: A 308 GLU cc_start: 0.7811 (pm20) cc_final: 0.7497 (pm20) REVERT: A 321 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7908 (mmmt) REVERT: A 340 ARG cc_start: 0.8822 (mtm-85) cc_final: 0.8596 (mpp-170) REVERT: C 66 ASP cc_start: 0.8083 (t0) cc_final: 0.7814 (t0) REVERT: C 72 ASN cc_start: 0.8280 (m-40) cc_final: 0.8014 (m110) REVERT: C 112 LYS cc_start: 0.7900 (mttp) cc_final: 0.7693 (mttp) REVERT: C 187 GLU cc_start: 0.7160 (tp30) cc_final: 0.6874 (mp0) REVERT: C 202 ASP cc_start: 0.7781 (m-30) cc_final: 0.7434 (m-30) REVERT: C 226 ASP cc_start: 0.7925 (t70) cc_final: 0.7653 (t70) REVERT: C 246 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7798 (mpp80) REVERT: C 258 LYS cc_start: 0.8943 (ptpp) cc_final: 0.8693 (ptpp) REVERT: C 308 GLU cc_start: 0.7861 (pm20) cc_final: 0.7491 (pm20) REVERT: D 41 GLU cc_start: 0.8017 (tt0) cc_final: 0.7803 (tt0) REVERT: D 132 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8304 (ttpt) REVERT: D 135 ARG cc_start: 0.8430 (tpp80) cc_final: 0.8090 (ttm-80) REVERT: D 159 LYS cc_start: 0.8647 (pttm) cc_final: 0.8259 (pttm) REVERT: D 258 LYS cc_start: 0.8889 (ptpp) cc_final: 0.8625 (ptpp) REVERT: D 308 GLU cc_start: 0.7863 (pm20) cc_final: 0.7514 (pm20) REVERT: D 321 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7991 (mtpp) REVERT: E 41 GLU cc_start: 0.7925 (tt0) cc_final: 0.7661 (tt0) REVERT: E 69 ASP cc_start: 0.7680 (m-30) cc_final: 0.7468 (m-30) REVERT: E 133 LYS cc_start: 0.8617 (tttm) cc_final: 0.8415 (tttp) REVERT: E 137 GLU cc_start: 0.7798 (mp0) cc_final: 0.7451 (mp0) REVERT: E 169 TYR cc_start: 0.7594 (m-80) cc_final: 0.7393 (m-10) REVERT: E 202 ASP cc_start: 0.7812 (m-30) cc_final: 0.7547 (m-30) REVERT: E 218 ASP cc_start: 0.7781 (m-30) cc_final: 0.7562 (m-30) REVERT: E 274 MET cc_start: 0.8520 (mtp) cc_final: 0.8243 (mtp) REVERT: E 302 MET cc_start: 0.8484 (tpp) cc_final: 0.8024 (tpp) REVERT: E 308 GLU cc_start: 0.7907 (pm20) cc_final: 0.7585 (pm20) REVERT: E 329 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7294 (mt-10) REVERT: F 54 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8313 (mtmm) REVERT: F 69 ASP cc_start: 0.7531 (m-30) cc_final: 0.7286 (m-30) REVERT: F 137 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7882 (mt-10) REVERT: F 244 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7808 (ttp-170) REVERT: F 246 ARG cc_start: 0.8242 (tpp80) cc_final: 0.7587 (mpp80) REVERT: F 286 LYS cc_start: 0.8629 (mttt) cc_final: 0.8414 (mttp) REVERT: F 308 GLU cc_start: 0.7841 (pm20) cc_final: 0.7496 (pm20) REVERT: F 332 LYS cc_start: 0.8608 (mttt) cc_final: 0.8292 (mttp) REVERT: G 37 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7496 (mt-10) REVERT: G 75 SER cc_start: 0.8673 (t) cc_final: 0.8411 (p) REVERT: G 90 GLU cc_start: 0.7664 (pm20) cc_final: 0.7291 (pm20) REVERT: G 133 LYS cc_start: 0.8738 (tttm) cc_final: 0.8364 (tttp) REVERT: G 137 GLU cc_start: 0.7843 (mp0) cc_final: 0.7329 (mp0) REVERT: G 218 ASP cc_start: 0.7773 (m-30) cc_final: 0.7484 (m-30) REVERT: G 246 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7763 (tpp80) REVERT: G 296 MET cc_start: 0.8301 (mpp) cc_final: 0.7803 (mpp) REVERT: G 329 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7010 (mt-10) REVERT: H 50 LYS cc_start: 0.8383 (tttp) cc_final: 0.8115 (tttm) REVERT: H 132 LYS cc_start: 0.8661 (ttpt) cc_final: 0.8453 (ttpt) REVERT: H 135 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8080 (ttp-170) REVERT: H 226 ASP cc_start: 0.7835 (t0) cc_final: 0.7564 (t0) REVERT: H 308 GLU cc_start: 0.7823 (pm20) cc_final: 0.7457 (pm20) outliers start: 62 outliers final: 29 residues processed: 802 average time/residue: 0.7997 time to fit residues: 701.3687 Evaluate side-chains 808 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 777 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 169 TYR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 169 TYR Chi-restraints excluded: chain H residue 329 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 30 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 218 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN C 63 ASN D 231 ASN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN F 231 ASN G 63 ASN G 249 ASN H 63 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.106110 restraints weight = 27867.652| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.95 r_work: 0.3290 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19776 Z= 0.155 Angle : 0.531 8.118 26808 Z= 0.289 Chirality : 0.047 0.158 2936 Planarity : 0.005 0.068 3464 Dihedral : 4.592 17.499 2672 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.85 % Allowed : 19.95 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.17), residues: 2424 helix: -2.33 (0.44), residues: 96 sheet: -0.01 (0.14), residues: 1384 loop : -1.43 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 135 TYR 0.021 0.001 TYR G 237 PHE 0.009 0.001 PHE D 100 TRP 0.009 0.001 TRP A 217 Details of bonding type rmsd covalent geometry : bond 0.00327 (19776) covalent geometry : angle 0.53118 (26808) hydrogen bonds : bond 0.03231 ( 936) hydrogen bonds : angle 4.89979 ( 3267) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 787 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.8668 (m-80) cc_final: 0.7808 (m-80) REVERT: B 69 ASP cc_start: 0.7702 (m-30) cc_final: 0.7463 (m-30) REVERT: B 72 ASN cc_start: 0.8328 (m-40) cc_final: 0.7926 (m-40) REVERT: B 75 SER cc_start: 0.8708 (t) cc_final: 0.8405 (p) REVERT: B 167 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8288 (tp) REVERT: B 202 ASP cc_start: 0.7880 (m-30) cc_final: 0.7504 (m-30) REVERT: B 258 LYS cc_start: 0.8950 (ptpp) cc_final: 0.8663 (ptpp) REVERT: B 308 GLU cc_start: 0.7610 (pm20) cc_final: 0.7150 (pm20) REVERT: A 135 ARG cc_start: 0.8435 (tpp80) cc_final: 0.8051 (tpp80) REVERT: A 159 LYS cc_start: 0.8491 (pttm) cc_final: 0.8098 (pttm) REVERT: A 226 ASP cc_start: 0.7760 (t0) cc_final: 0.7327 (t70) REVERT: A 308 GLU cc_start: 0.7717 (pm20) cc_final: 0.7413 (pm20) REVERT: A 321 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7752 (mmmt) REVERT: A 328 TYR cc_start: 0.8549 (t80) cc_final: 0.8316 (t80) REVERT: C 33 VAL cc_start: 0.8709 (p) cc_final: 0.8403 (t) REVERT: C 66 ASP cc_start: 0.8030 (t0) cc_final: 0.7771 (t0) REVERT: C 72 ASN cc_start: 0.8277 (m-40) cc_final: 0.7873 (m110) REVERT: C 202 ASP cc_start: 0.7741 (m-30) cc_final: 0.7437 (m-30) REVERT: C 203 TYR cc_start: 0.8830 (m-80) cc_final: 0.8601 (m-80) REVERT: C 226 ASP cc_start: 0.7883 (t70) cc_final: 0.7623 (t70) REVERT: C 258 LYS cc_start: 0.8950 (ptpp) cc_final: 0.8712 (ptpp) REVERT: C 308 GLU cc_start: 0.7808 (pm20) cc_final: 0.7397 (pm20) REVERT: C 322 GLU cc_start: 0.8332 (pt0) cc_final: 0.8051 (pt0) REVERT: C 329 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6978 (mt-10) REVERT: D 41 GLU cc_start: 0.7959 (tt0) cc_final: 0.7744 (tt0) REVERT: D 114 LYS cc_start: 0.7217 (mmtp) cc_final: 0.7003 (mmtp) REVERT: D 246 ARG cc_start: 0.7599 (ttm-80) cc_final: 0.7246 (ttm-80) REVERT: D 258 LYS cc_start: 0.8862 (ptpp) cc_final: 0.8594 (ptpp) REVERT: D 308 GLU cc_start: 0.7721 (pm20) cc_final: 0.7389 (pm20) REVERT: E 41 GLU cc_start: 0.7871 (tt0) cc_final: 0.7616 (tt0) REVERT: E 69 ASP cc_start: 0.7682 (m-30) cc_final: 0.7452 (m-30) REVERT: E 137 GLU cc_start: 0.7724 (mp0) cc_final: 0.7398 (mp0) REVERT: E 202 ASP cc_start: 0.7802 (m-30) cc_final: 0.7472 (m-30) REVERT: E 308 GLU cc_start: 0.7826 (pm20) cc_final: 0.7483 (pm20) REVERT: F 54 LYS cc_start: 0.8552 (mtpp) cc_final: 0.8286 (mtmm) REVERT: F 66 ASP cc_start: 0.8109 (t0) cc_final: 0.7903 (t0) REVERT: F 69 ASP cc_start: 0.7462 (m-30) cc_final: 0.7233 (m-30) REVERT: F 137 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7918 (mt-10) REVERT: F 246 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7740 (mpp80) REVERT: F 308 GLU cc_start: 0.7723 (pm20) cc_final: 0.7362 (pm20) REVERT: F 332 LYS cc_start: 0.8555 (mttt) cc_final: 0.8245 (mttp) REVERT: G 33 VAL cc_start: 0.8682 (p) cc_final: 0.8377 (t) REVERT: G 37 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7351 (mt-10) REVERT: G 75 SER cc_start: 0.8661 (t) cc_final: 0.8391 (p) REVERT: G 90 GLU cc_start: 0.7571 (pm20) cc_final: 0.7224 (pm20) REVERT: G 133 LYS cc_start: 0.8667 (tttm) cc_final: 0.8466 (tttp) REVERT: G 137 GLU cc_start: 0.7770 (mp0) cc_final: 0.7318 (mp0) REVERT: G 209 LYS cc_start: 0.8755 (tttp) cc_final: 0.8530 (ttmm) REVERT: G 218 ASP cc_start: 0.7673 (m-30) cc_final: 0.7452 (m-30) REVERT: G 329 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6922 (mt-10) REVERT: H 50 LYS cc_start: 0.8275 (tttp) cc_final: 0.7955 (tttm) REVERT: H 135 ARG cc_start: 0.8372 (tpp80) cc_final: 0.7969 (ttp-170) REVERT: H 144 ASP cc_start: 0.7575 (m-30) cc_final: 0.7363 (m-30) REVERT: H 159 LYS cc_start: 0.8458 (pttm) cc_final: 0.7841 (pttm) REVERT: H 226 ASP cc_start: 0.7766 (t0) cc_final: 0.7484 (t0) REVERT: H 303 ARG cc_start: 0.8506 (mtt90) cc_final: 0.8269 (mtt180) REVERT: H 308 GLU cc_start: 0.7700 (pm20) cc_final: 0.7371 (pm20) outliers start: 40 outliers final: 20 residues processed: 796 average time/residue: 0.8045 time to fit residues: 699.5038 Evaluate side-chains 789 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 768 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 329 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 31 optimal weight: 0.5980 chunk 157 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 223 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 44 optimal weight: 0.4980 chunk 158 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN E 316 ASN G 316 ASN H 63 ASN H 316 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.106718 restraints weight = 27590.442| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.93 r_work: 0.3304 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19776 Z= 0.149 Angle : 0.538 8.059 26808 Z= 0.291 Chirality : 0.047 0.156 2936 Planarity : 0.005 0.066 3464 Dihedral : 4.497 17.127 2672 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.81 % Allowed : 21.57 % Favored : 76.62 % 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: -0.96 (0.17), residues: 2424 helix: -2.31 (0.44), residues: 96 sheet: 0.08 (0.14), residues: 1400 loop : -1.50 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 135 TYR 0.021 0.001 TYR B 237 PHE 0.010 0.001 PHE H 242 TRP 0.008 0.001 TRP A 217 Details of bonding type rmsd covalent geometry : bond 0.00320 (19776) covalent geometry : angle 0.53829 (26808) hydrogen bonds : bond 0.03174 ( 936) hydrogen bonds : angle 4.77055 ( 3267) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 779 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.8648 (m-80) cc_final: 0.7876 (m-80) REVERT: B 69 ASP cc_start: 0.7660 (m-30) cc_final: 0.7441 (m-30) REVERT: B 72 ASN cc_start: 0.8270 (m-40) cc_final: 0.7862 (m-40) REVERT: B 75 SER cc_start: 0.8690 (t) cc_final: 0.8385 (p) REVERT: B 132 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8285 (ttpt) REVERT: B 167 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8320 (tp) REVERT: B 202 ASP cc_start: 0.7893 (m-30) cc_final: 0.7533 (m-30) REVERT: B 246 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7667 (mtm180) REVERT: B 258 LYS cc_start: 0.8935 (ptpp) cc_final: 0.8657 (ptpp) REVERT: B 308 GLU cc_start: 0.7647 (pm20) cc_final: 0.7283 (pm20) REVERT: A 135 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8088 (tpp80) REVERT: A 159 LYS cc_start: 0.8490 (pttm) cc_final: 0.8093 (pttm) REVERT: A 226 ASP cc_start: 0.7699 (t0) cc_final: 0.7276 (t70) REVERT: A 308 GLU cc_start: 0.7734 (pm20) cc_final: 0.7439 (pm20) REVERT: A 321 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7688 (mmmt) REVERT: A 328 TYR cc_start: 0.8563 (t80) cc_final: 0.8351 (t80) REVERT: A 336 ASP cc_start: 0.7870 (t0) cc_final: 0.7664 (t0) REVERT: A 340 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.8560 (mtt90) REVERT: C 33 VAL cc_start: 0.8719 (p) cc_final: 0.8413 (t) REVERT: C 66 ASP cc_start: 0.8043 (t0) cc_final: 0.7822 (t0) REVERT: C 72 ASN cc_start: 0.8240 (m-40) cc_final: 0.7536 (m-40) REVERT: C 202 ASP cc_start: 0.7768 (m-30) cc_final: 0.7481 (m-30) REVERT: C 203 TYR cc_start: 0.8848 (m-80) cc_final: 0.8621 (m-80) REVERT: C 226 ASP cc_start: 0.7922 (t70) cc_final: 0.7665 (t70) REVERT: C 258 LYS cc_start: 0.8921 (ptpp) cc_final: 0.8690 (ptpp) REVERT: C 296 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7855 (mtm) REVERT: C 303 ARG cc_start: 0.8664 (mtt90) cc_final: 0.8435 (mtt180) REVERT: C 308 GLU cc_start: 0.7812 (pm20) cc_final: 0.7381 (pm20) REVERT: C 322 GLU cc_start: 0.8360 (pt0) cc_final: 0.8103 (pt0) REVERT: C 329 GLU cc_start: 0.7551 (mt-10) cc_final: 0.6872 (mt-10) REVERT: D 41 GLU cc_start: 0.7947 (tt0) cc_final: 0.7743 (tt0) REVERT: D 246 ARG cc_start: 0.7638 (ttm-80) cc_final: 0.7294 (ttm-80) REVERT: D 258 LYS cc_start: 0.8851 (ptpp) cc_final: 0.8589 (ptpp) REVERT: D 274 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8130 (mtp) REVERT: D 308 GLU cc_start: 0.7712 (pm20) cc_final: 0.7392 (pm20) REVERT: E 41 GLU cc_start: 0.7912 (tt0) cc_final: 0.7655 (tt0) REVERT: E 137 GLU cc_start: 0.7688 (mp0) cc_final: 0.7311 (mp0) REVERT: E 202 ASP cc_start: 0.7807 (m-30) cc_final: 0.7473 (m-30) REVERT: E 308 GLU cc_start: 0.7854 (pm20) cc_final: 0.7527 (pm20) REVERT: E 329 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7246 (mt-10) REVERT: F 54 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8254 (mtmm) REVERT: F 69 ASP cc_start: 0.7431 (m-30) cc_final: 0.7218 (m-30) REVERT: F 137 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7938 (mt-10) REVERT: F 246 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7746 (tpp80) REVERT: F 308 GLU cc_start: 0.7715 (pm20) cc_final: 0.7378 (pm20) REVERT: F 332 LYS cc_start: 0.8594 (mttt) cc_final: 0.8288 (mttp) REVERT: G 33 VAL cc_start: 0.8675 (p) cc_final: 0.8377 (t) REVERT: G 37 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7359 (mt-10) REVERT: G 75 SER cc_start: 0.8658 (t) cc_final: 0.8393 (p) REVERT: G 90 GLU cc_start: 0.7471 (pm20) cc_final: 0.7131 (pm20) REVERT: G 137 GLU cc_start: 0.7788 (mp0) cc_final: 0.7335 (mp0) REVERT: G 329 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6962 (mt-10) REVERT: H 50 LYS cc_start: 0.8262 (tttp) cc_final: 0.7956 (tttm) REVERT: H 135 ARG cc_start: 0.8343 (tpp80) cc_final: 0.7960 (ttp-170) REVERT: H 144 ASP cc_start: 0.7609 (m-30) cc_final: 0.7398 (m-30) REVERT: H 159 LYS cc_start: 0.8514 (pttm) cc_final: 0.7980 (pttm) REVERT: H 226 ASP cc_start: 0.7782 (t0) cc_final: 0.7452 (t0) REVERT: H 308 GLU cc_start: 0.7766 (pm20) cc_final: 0.7466 (pm20) outliers start: 39 outliers final: 20 residues processed: 787 average time/residue: 0.8180 time to fit residues: 701.7394 Evaluate side-chains 793 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 769 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 151 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 54 optimal weight: 0.0970 chunk 175 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 132 optimal weight: 0.4980 chunk 110 optimal weight: 7.9990 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN E 63 ASN H 63 ASN H 72 ASN H 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.105836 restraints weight = 27825.989| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.92 r_work: 0.3303 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19776 Z= 0.221 Angle : 0.578 8.696 26808 Z= 0.310 Chirality : 0.048 0.160 2936 Planarity : 0.005 0.066 3464 Dihedral : 4.663 18.794 2672 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.99 % Allowed : 22.31 % Favored : 75.69 % 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: -0.96 (0.17), residues: 2424 helix: -2.26 (0.44), residues: 96 sheet: 0.08 (0.14), residues: 1400 loop : -1.50 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 135 TYR 0.038 0.002 TYR B 237 PHE 0.009 0.001 PHE B 333 TRP 0.007 0.001 TRP H 337 Details of bonding type rmsd covalent geometry : bond 0.00475 (19776) covalent geometry : angle 0.57833 (26808) hydrogen bonds : bond 0.03394 ( 936) hydrogen bonds : angle 4.83451 ( 3267) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 764 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.7584 (m-30) cc_final: 0.7367 (m-30) REVERT: B 72 ASN cc_start: 0.8272 (m-40) cc_final: 0.7815 (m110) REVERT: B 75 SER cc_start: 0.8690 (t) cc_final: 0.8372 (p) REVERT: B 202 ASP cc_start: 0.8000 (m-30) cc_final: 0.7613 (m-30) REVERT: B 258 LYS cc_start: 0.8900 (ptpp) cc_final: 0.8674 (ptpp) REVERT: B 308 GLU cc_start: 0.7768 (pm20) cc_final: 0.7395 (pm20) REVERT: A 159 LYS cc_start: 0.8492 (pttm) cc_final: 0.8055 (pttm) REVERT: A 226 ASP cc_start: 0.7792 (t0) cc_final: 0.7341 (t0) REVERT: A 308 GLU cc_start: 0.7811 (pm20) cc_final: 0.7500 (pm20) REVERT: A 321 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7771 (mmmt) REVERT: C 33 VAL cc_start: 0.8697 (p) cc_final: 0.8402 (t) REVERT: C 66 ASP cc_start: 0.8119 (t0) cc_final: 0.7871 (t0) REVERT: C 72 ASN cc_start: 0.8213 (m-40) cc_final: 0.7896 (m-40) REVERT: C 202 ASP cc_start: 0.7862 (m-30) cc_final: 0.7558 (m-30) REVERT: C 226 ASP cc_start: 0.7957 (t70) cc_final: 0.7680 (t70) REVERT: C 258 LYS cc_start: 0.8885 (ptpp) cc_final: 0.8636 (ptpp) REVERT: C 296 MET cc_start: 0.7974 (mtm) cc_final: 0.7676 (mtm) REVERT: C 308 GLU cc_start: 0.7838 (pm20) cc_final: 0.7395 (pm20) REVERT: C 322 GLU cc_start: 0.8316 (pt0) cc_final: 0.8049 (pt0) REVERT: D 41 GLU cc_start: 0.7958 (tt0) cc_final: 0.7745 (tt0) REVERT: D 132 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8212 (ttpt) REVERT: D 258 LYS cc_start: 0.8864 (ptpp) cc_final: 0.8591 (ptpp) REVERT: D 308 GLU cc_start: 0.7779 (pm20) cc_final: 0.7449 (pm20) REVERT: D 321 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7875 (mtpp) REVERT: E 41 GLU cc_start: 0.7891 (tt0) cc_final: 0.7611 (tt0) REVERT: E 133 LYS cc_start: 0.8567 (tttp) cc_final: 0.8323 (tttp) REVERT: E 137 GLU cc_start: 0.7663 (mp0) cc_final: 0.7276 (mp0) REVERT: E 202 ASP cc_start: 0.7926 (m-30) cc_final: 0.7575 (m-30) REVERT: E 308 GLU cc_start: 0.7896 (pm20) cc_final: 0.7560 (pm20) REVERT: E 329 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7195 (mt-10) REVERT: E 330 ASP cc_start: 0.8002 (p0) cc_final: 0.7799 (p0) REVERT: F 54 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8222 (mtmm) REVERT: F 69 ASP cc_start: 0.7497 (m-30) cc_final: 0.7276 (m-30) REVERT: F 106 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8044 (mtp180) REVERT: F 246 ARG cc_start: 0.8055 (tpp80) cc_final: 0.7697 (mpp80) REVERT: F 308 GLU cc_start: 0.7776 (pm20) cc_final: 0.7428 (pm20) REVERT: F 332 LYS cc_start: 0.8635 (mttt) cc_final: 0.8329 (mttp) REVERT: G 33 VAL cc_start: 0.8665 (p) cc_final: 0.8366 (t) REVERT: G 37 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7288 (mt-10) REVERT: G 75 SER cc_start: 0.8648 (t) cc_final: 0.8381 (p) REVERT: G 90 GLU cc_start: 0.7487 (pm20) cc_final: 0.7150 (pm20) REVERT: G 133 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8303 (tttp) REVERT: G 137 GLU cc_start: 0.7668 (mp0) cc_final: 0.7197 (mp0) REVERT: G 299 MET cc_start: 0.8405 (tpp) cc_final: 0.8075 (mmt) REVERT: G 329 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6973 (mt-10) REVERT: H 50 LYS cc_start: 0.8314 (tttp) cc_final: 0.7671 (tttm) REVERT: H 135 ARG cc_start: 0.8381 (tpp80) cc_final: 0.8085 (ttp-170) REVERT: H 159 LYS cc_start: 0.8512 (pttm) cc_final: 0.8026 (pttm) REVERT: H 226 ASP cc_start: 0.7813 (t0) cc_final: 0.7459 (t0) REVERT: H 308 GLU cc_start: 0.7746 (pm20) cc_final: 0.7430 (pm20) outliers start: 43 outliers final: 23 residues processed: 778 average time/residue: 0.7953 time to fit residues: 675.3834 Evaluate side-chains 776 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 751 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 133 LYS Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 329 GLU Chi-restraints excluded: chain H residue 338 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN F 231 ASN H 63 ASN H 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.107082 restraints weight = 27857.907| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.93 r_work: 0.3319 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19776 Z= 0.162 Angle : 0.557 8.689 26808 Z= 0.302 Chirality : 0.048 0.157 2936 Planarity : 0.005 0.065 3464 Dihedral : 4.572 18.605 2672 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.53 % Allowed : 23.52 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.17), residues: 2424 helix: -2.27 (0.43), residues: 96 sheet: 0.06 (0.14), residues: 1400 loop : -1.46 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 135 TYR 0.031 0.001 TYR B 237 PHE 0.009 0.001 PHE D 100 TRP 0.007 0.001 TRP A 217 Details of bonding type rmsd covalent geometry : bond 0.00350 (19776) covalent geometry : angle 0.55659 (26808) hydrogen bonds : bond 0.03228 ( 936) hydrogen bonds : angle 4.77353 ( 3267) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 764 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: B 69 ASP cc_start: 0.7610 (m-30) cc_final: 0.7379 (m-30) REVERT: B 72 ASN cc_start: 0.8249 (m-40) cc_final: 0.7817 (m110) REVERT: B 75 SER cc_start: 0.8691 (t) cc_final: 0.8371 (p) REVERT: B 202 ASP cc_start: 0.8006 (m-30) cc_final: 0.7626 (m-30) REVERT: B 258 LYS cc_start: 0.8886 (ptpp) cc_final: 0.8574 (ptpp) REVERT: B 308 GLU cc_start: 0.7761 (pm20) cc_final: 0.7374 (pm20) REVERT: A 133 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8310 (tttm) REVERT: A 135 ARG cc_start: 0.8375 (tpp80) cc_final: 0.8085 (tpp80) REVERT: A 159 LYS cc_start: 0.8442 (pttm) cc_final: 0.8027 (pttm) REVERT: A 226 ASP cc_start: 0.7753 (t0) cc_final: 0.7312 (t70) REVERT: A 308 GLU cc_start: 0.7774 (pm20) cc_final: 0.7464 (pm20) REVERT: A 321 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7736 (mmmt) REVERT: C 33 VAL cc_start: 0.8685 (p) cc_final: 0.8373 (t) REVERT: C 66 ASP cc_start: 0.8115 (t0) cc_final: 0.7798 (t0) REVERT: C 72 ASN cc_start: 0.8203 (m-40) cc_final: 0.7495 (m-40) REVERT: C 202 ASP cc_start: 0.7853 (m-30) cc_final: 0.7551 (m-30) REVERT: C 226 ASP cc_start: 0.7952 (t70) cc_final: 0.7670 (t70) REVERT: C 258 LYS cc_start: 0.8888 (ptpp) cc_final: 0.8657 (ptpp) REVERT: C 303 ARG cc_start: 0.8670 (mtt90) cc_final: 0.8456 (mtt180) REVERT: C 308 GLU cc_start: 0.7832 (pm20) cc_final: 0.7374 (pm20) REVERT: C 322 GLU cc_start: 0.8335 (pt0) cc_final: 0.8086 (pt0) REVERT: C 329 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6827 (mt-10) REVERT: D 41 GLU cc_start: 0.7920 (tt0) cc_final: 0.7708 (tt0) REVERT: D 132 LYS cc_start: 0.8483 (ttmt) cc_final: 0.8174 (ttpt) REVERT: D 258 LYS cc_start: 0.8852 (ptpp) cc_final: 0.8582 (ptpp) REVERT: D 308 GLU cc_start: 0.7712 (pm20) cc_final: 0.7374 (pm20) REVERT: D 321 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7840 (mtpp) REVERT: E 41 GLU cc_start: 0.7919 (tt0) cc_final: 0.7657 (tt0) REVERT: E 133 LYS cc_start: 0.8572 (tttp) cc_final: 0.8294 (tttp) REVERT: E 135 ARG cc_start: 0.8433 (tpp80) cc_final: 0.8147 (tpp80) REVERT: E 137 GLU cc_start: 0.7646 (mp0) cc_final: 0.7240 (mp0) REVERT: E 202 ASP cc_start: 0.7899 (m-30) cc_final: 0.7555 (m-30) REVERT: E 296 MET cc_start: 0.8178 (mpp) cc_final: 0.7690 (mpp) REVERT: E 308 GLU cc_start: 0.7866 (pm20) cc_final: 0.7519 (pm20) REVERT: E 330 ASP cc_start: 0.7946 (p0) cc_final: 0.7730 (p0) REVERT: F 54 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8238 (mtmm) REVERT: F 69 ASP cc_start: 0.7476 (m-30) cc_final: 0.7252 (m-30) REVERT: F 106 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8043 (mtp180) REVERT: F 167 ILE cc_start: 0.8470 (mp) cc_final: 0.8127 (mp) REVERT: F 246 ARG cc_start: 0.7897 (tpp80) cc_final: 0.7680 (mpp80) REVERT: F 285 LYS cc_start: 0.8231 (mttm) cc_final: 0.7991 (mtpp) REVERT: F 308 GLU cc_start: 0.7764 (pm20) cc_final: 0.7418 (pm20) REVERT: F 332 LYS cc_start: 0.8627 (mttt) cc_final: 0.8313 (mttp) REVERT: G 33 VAL cc_start: 0.8681 (p) cc_final: 0.8379 (t) REVERT: G 37 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7410 (mt-10) REVERT: G 75 SER cc_start: 0.8659 (t) cc_final: 0.8398 (p) REVERT: G 90 GLU cc_start: 0.7415 (pm20) cc_final: 0.7085 (pm20) REVERT: G 133 LYS cc_start: 0.8594 (tptm) cc_final: 0.8323 (tttp) REVERT: G 137 GLU cc_start: 0.7647 (mp0) cc_final: 0.7218 (mp0) REVERT: G 258 LYS cc_start: 0.8925 (ptpp) cc_final: 0.8412 (pttm) REVERT: G 329 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6914 (mt-10) REVERT: H 50 LYS cc_start: 0.8287 (tttp) cc_final: 0.8077 (tttm) REVERT: H 132 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8151 (ttmt) REVERT: H 135 ARG cc_start: 0.8344 (tpp80) cc_final: 0.8108 (ttp-170) REVERT: H 144 ASP cc_start: 0.7667 (m-30) cc_final: 0.7451 (m-30) REVERT: H 159 LYS cc_start: 0.8538 (pttm) cc_final: 0.8098 (pttm) REVERT: H 208 ILE cc_start: 0.8701 (pt) cc_final: 0.8483 (pt) REVERT: H 226 ASP cc_start: 0.7757 (t0) cc_final: 0.7417 (t0) REVERT: H 298 ASP cc_start: 0.8047 (m-30) cc_final: 0.7633 (m-30) REVERT: H 308 GLU cc_start: 0.7720 (pm20) cc_final: 0.7399 (pm20) outliers start: 33 outliers final: 22 residues processed: 775 average time/residue: 0.7728 time to fit residues: 653.8329 Evaluate side-chains 779 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 755 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 329 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 113 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 187 optimal weight: 0.2980 chunk 182 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN D 72 ASN E 72 ASN E 231 ASN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106211 restraints weight = 27808.275| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.90 r_work: 0.3313 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19776 Z= 0.195 Angle : 0.579 8.923 26808 Z= 0.313 Chirality : 0.048 0.159 2936 Planarity : 0.005 0.065 3464 Dihedral : 4.658 19.250 2672 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.67 % Allowed : 23.52 % Favored : 74.81 % 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: -0.96 (0.17), residues: 2424 helix: -2.26 (0.43), residues: 96 sheet: 0.07 (0.14), residues: 1400 loop : -1.48 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 135 TYR 0.039 0.001 TYR B 237 PHE 0.008 0.001 PHE D 100 TRP 0.006 0.001 TRP H 337 Details of bonding type rmsd covalent geometry : bond 0.00422 (19776) covalent geometry : angle 0.57924 (26808) hydrogen bonds : bond 0.03327 ( 936) hydrogen bonds : angle 4.80172 ( 3267) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 758 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.7616 (m-30) cc_final: 0.7394 (m-30) REVERT: B 75 SER cc_start: 0.8696 (t) cc_final: 0.8372 (p) REVERT: B 202 ASP cc_start: 0.7999 (m-30) cc_final: 0.7636 (m-30) REVERT: B 258 LYS cc_start: 0.8903 (ptpp) cc_final: 0.8594 (ptpp) REVERT: B 308 GLU cc_start: 0.7793 (pm20) cc_final: 0.7454 (pm20) REVERT: A 39 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8251 (m) REVERT: A 135 ARG cc_start: 0.8369 (tpp80) cc_final: 0.8089 (tpp80) REVERT: A 159 LYS cc_start: 0.8471 (pttm) cc_final: 0.8044 (pttm) REVERT: A 226 ASP cc_start: 0.7766 (t0) cc_final: 0.7327 (t70) REVERT: A 308 GLU cc_start: 0.7750 (pm20) cc_final: 0.7444 (pm20) REVERT: A 321 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7748 (mmmt) REVERT: C 33 VAL cc_start: 0.8699 (p) cc_final: 0.8391 (t) REVERT: C 66 ASP cc_start: 0.8117 (t0) cc_final: 0.7823 (t0) REVERT: C 72 ASN cc_start: 0.8224 (m-40) cc_final: 0.7590 (m-40) REVERT: C 202 ASP cc_start: 0.7832 (m-30) cc_final: 0.7517 (m-30) REVERT: C 226 ASP cc_start: 0.7929 (t70) cc_final: 0.7649 (t70) REVERT: C 246 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7279 (mtt90) REVERT: C 258 LYS cc_start: 0.8888 (ptpp) cc_final: 0.8643 (ptpp) REVERT: C 308 GLU cc_start: 0.7837 (pm20) cc_final: 0.7373 (pm20) REVERT: C 322 GLU cc_start: 0.8335 (pt0) cc_final: 0.8089 (pt0) REVERT: D 41 GLU cc_start: 0.7972 (tt0) cc_final: 0.7763 (tt0) REVERT: D 132 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8170 (ttpt) REVERT: D 258 LYS cc_start: 0.8872 (ptpp) cc_final: 0.8608 (ptpp) REVERT: D 308 GLU cc_start: 0.7756 (pm20) cc_final: 0.7413 (pm20) REVERT: D 321 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7848 (mtpp) REVERT: E 41 GLU cc_start: 0.7890 (tt0) cc_final: 0.7635 (tt0) REVERT: E 133 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8150 (tttp) REVERT: E 137 GLU cc_start: 0.7615 (mp0) cc_final: 0.7182 (mp0) REVERT: E 202 ASP cc_start: 0.7892 (m-30) cc_final: 0.7544 (m-30) REVERT: E 296 MET cc_start: 0.8196 (mpp) cc_final: 0.7652 (mpp) REVERT: E 308 GLU cc_start: 0.7853 (pm20) cc_final: 0.7518 (pm20) REVERT: E 330 ASP cc_start: 0.7955 (p0) cc_final: 0.7734 (p0) REVERT: F 54 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8233 (mtmm) REVERT: F 69 ASP cc_start: 0.7460 (m-30) cc_final: 0.7238 (m-30) REVERT: F 106 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8061 (mtp180) REVERT: F 246 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7675 (mpp80) REVERT: F 285 LYS cc_start: 0.8235 (mttm) cc_final: 0.7988 (mtpp) REVERT: F 308 GLU cc_start: 0.7762 (pm20) cc_final: 0.7413 (pm20) REVERT: F 329 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6946 (mt-10) REVERT: F 332 LYS cc_start: 0.8614 (mttt) cc_final: 0.8334 (mtmm) REVERT: G 33 VAL cc_start: 0.8683 (p) cc_final: 0.8381 (t) REVERT: G 75 SER cc_start: 0.8667 (t) cc_final: 0.8397 (p) REVERT: G 90 GLU cc_start: 0.7367 (pm20) cc_final: 0.7030 (pm20) REVERT: G 133 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8312 (tttp) REVERT: G 137 GLU cc_start: 0.7649 (mp0) cc_final: 0.7206 (mp0) REVERT: G 329 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6937 (mt-10) REVERT: H 90 GLU cc_start: 0.7322 (pm20) cc_final: 0.6883 (pm20) REVERT: H 132 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8326 (ttmt) REVERT: H 135 ARG cc_start: 0.8379 (tpp80) cc_final: 0.8114 (ttp-170) REVERT: H 159 LYS cc_start: 0.8549 (pttm) cc_final: 0.8129 (pttm) REVERT: H 208 ILE cc_start: 0.8710 (pt) cc_final: 0.8503 (pt) REVERT: H 226 ASP cc_start: 0.7795 (t0) cc_final: 0.7490 (t0) REVERT: H 298 ASP cc_start: 0.8060 (m-30) cc_final: 0.7860 (m-30) REVERT: H 308 GLU cc_start: 0.7738 (pm20) cc_final: 0.7421 (pm20) outliers start: 36 outliers final: 24 residues processed: 770 average time/residue: 0.7896 time to fit residues: 663.5778 Evaluate side-chains 793 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 763 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 133 LYS Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 274 MET Chi-restraints excluded: chain H residue 329 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 196 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 223 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN D 72 ASN D 316 ASN E 231 ASN F 231 ASN G 56 GLN H 63 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.107096 restraints weight = 27783.654| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.92 r_work: 0.3320 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19776 Z= 0.172 Angle : 0.581 11.479 26808 Z= 0.313 Chirality : 0.048 0.158 2936 Planarity : 0.005 0.066 3464 Dihedral : 4.653 21.046 2672 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.44 % Allowed : 23.89 % Favored : 74.68 % 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: -0.96 (0.17), residues: 2424 helix: -2.25 (0.43), residues: 96 sheet: 0.07 (0.14), residues: 1400 loop : -1.47 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 135 TYR 0.036 0.001 TYR B 237 PHE 0.009 0.001 PHE D 100 TRP 0.006 0.001 TRP H 217 Details of bonding type rmsd covalent geometry : bond 0.00373 (19776) covalent geometry : angle 0.58078 (26808) hydrogen bonds : bond 0.03274 ( 936) hydrogen bonds : angle 4.79172 ( 3267) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 769 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.7576 (m-30) cc_final: 0.7361 (m-30) REVERT: B 75 SER cc_start: 0.8700 (t) cc_final: 0.8370 (p) REVERT: B 202 ASP cc_start: 0.7992 (m-30) cc_final: 0.7638 (m-30) REVERT: B 258 LYS cc_start: 0.8923 (ptpp) cc_final: 0.8638 (ptpp) REVERT: B 308 GLU cc_start: 0.7785 (pm20) cc_final: 0.7478 (pm20) REVERT: A 226 ASP cc_start: 0.7780 (t0) cc_final: 0.7342 (t70) REVERT: A 308 GLU cc_start: 0.7750 (pm20) cc_final: 0.7440 (pm20) REVERT: A 321 LYS cc_start: 0.7977 (mtmt) cc_final: 0.7733 (mmmt) REVERT: C 66 ASP cc_start: 0.8109 (t0) cc_final: 0.7795 (t0) REVERT: C 72 ASN cc_start: 0.8212 (m-40) cc_final: 0.7501 (m-40) REVERT: C 133 LYS cc_start: 0.8581 (ptmm) cc_final: 0.8307 (ptmm) REVERT: C 202 ASP cc_start: 0.7843 (m-30) cc_final: 0.7495 (m-30) REVERT: C 226 ASP cc_start: 0.7924 (t70) cc_final: 0.7645 (t70) REVERT: C 258 LYS cc_start: 0.8882 (ptpp) cc_final: 0.8649 (ptpp) REVERT: C 303 ARG cc_start: 0.8704 (mtt90) cc_final: 0.8318 (mtt180) REVERT: C 308 GLU cc_start: 0.7864 (pm20) cc_final: 0.7402 (pm20) REVERT: C 322 GLU cc_start: 0.8329 (pt0) cc_final: 0.8086 (pt0) REVERT: C 329 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6816 (mt-10) REVERT: D 41 GLU cc_start: 0.7969 (tt0) cc_final: 0.7747 (tt0) REVERT: D 237 TYR cc_start: 0.8471 (m-10) cc_final: 0.8267 (m-10) REVERT: D 258 LYS cc_start: 0.8873 (ptpp) cc_final: 0.8604 (ptpp) REVERT: D 300 TYR cc_start: 0.8538 (t80) cc_final: 0.8274 (t80) REVERT: D 308 GLU cc_start: 0.7738 (pm20) cc_final: 0.7392 (pm20) REVERT: E 41 GLU cc_start: 0.7863 (tt0) cc_final: 0.7626 (tt0) REVERT: E 133 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8262 (tttp) REVERT: E 135 ARG cc_start: 0.8387 (tpp80) cc_final: 0.8015 (tpp-160) REVERT: E 137 GLU cc_start: 0.7618 (mp0) cc_final: 0.7182 (mp0) REVERT: E 202 ASP cc_start: 0.7908 (m-30) cc_final: 0.7552 (m-30) REVERT: E 308 GLU cc_start: 0.7848 (pm20) cc_final: 0.7500 (pm20) REVERT: E 330 ASP cc_start: 0.7978 (p0) cc_final: 0.7767 (p0) REVERT: F 54 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8225 (mtmm) REVERT: F 69 ASP cc_start: 0.7466 (m-30) cc_final: 0.7245 (m-30) REVERT: F 106 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8064 (mtp180) REVERT: F 285 LYS cc_start: 0.8217 (mttm) cc_final: 0.7966 (mtpp) REVERT: F 308 GLU cc_start: 0.7760 (pm20) cc_final: 0.7417 (pm20) REVERT: F 329 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6979 (mt-10) REVERT: F 332 LYS cc_start: 0.8620 (mttt) cc_final: 0.8334 (mtmm) REVERT: G 33 VAL cc_start: 0.8695 (p) cc_final: 0.8400 (t) REVERT: G 75 SER cc_start: 0.8680 (t) cc_final: 0.8405 (p) REVERT: G 90 GLU cc_start: 0.7337 (pm20) cc_final: 0.7013 (pm20) REVERT: G 133 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8408 (tttp) REVERT: G 137 GLU cc_start: 0.7660 (mp0) cc_final: 0.7231 (mp0) REVERT: G 258 LYS cc_start: 0.8922 (ptpp) cc_final: 0.8432 (pttm) REVERT: G 301 ILE cc_start: 0.8830 (mp) cc_final: 0.8584 (mt) REVERT: G 329 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6934 (mt-10) REVERT: H 90 GLU cc_start: 0.7252 (pm20) cc_final: 0.6850 (pm20) REVERT: H 132 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8303 (ttmt) REVERT: H 135 ARG cc_start: 0.8369 (tpp80) cc_final: 0.8112 (ttp-170) REVERT: H 144 ASP cc_start: 0.7665 (m-30) cc_final: 0.7457 (m-30) REVERT: H 159 LYS cc_start: 0.8538 (pttm) cc_final: 0.8144 (pttm) REVERT: H 208 ILE cc_start: 0.8711 (pt) cc_final: 0.8489 (pt) REVERT: H 226 ASP cc_start: 0.7788 (t0) cc_final: 0.7487 (t70) REVERT: H 308 GLU cc_start: 0.7709 (pm20) cc_final: 0.7390 (pm20) REVERT: H 328 TYR cc_start: 0.8454 (t80) cc_final: 0.8248 (t80) outliers start: 31 outliers final: 22 residues processed: 779 average time/residue: 0.8036 time to fit residues: 683.4718 Evaluate side-chains 798 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 773 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 133 LYS Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 274 MET Chi-restraints excluded: chain H residue 329 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 182 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 109 optimal weight: 0.0670 chunk 116 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN E 231 ASN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105974 restraints weight = 27843.971| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.91 r_work: 0.3305 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19776 Z= 0.230 Angle : 0.610 12.024 26808 Z= 0.327 Chirality : 0.049 0.163 2936 Planarity : 0.006 0.066 3464 Dihedral : 4.792 21.323 2672 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.30 % Allowed : 24.35 % Favored : 74.35 % 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: -0.98 (0.17), residues: 2424 helix: -2.26 (0.43), residues: 96 sheet: 0.05 (0.14), residues: 1400 loop : -1.48 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 246 TYR 0.043 0.002 TYR B 237 PHE 0.011 0.001 PHE F 242 TRP 0.007 0.001 TRP H 337 Details of bonding type rmsd covalent geometry : bond 0.00499 (19776) covalent geometry : angle 0.61001 (26808) hydrogen bonds : bond 0.03435 ( 936) hydrogen bonds : angle 4.84404 ( 3267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10355.05 seconds wall clock time: 176 minutes 2.31 seconds (10562.31 seconds total)