Starting phenix.real_space_refine on Wed Jun 25 01:53:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4e_25673/06_2025/7t4e_25673.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4e_25673/06_2025/7t4e_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_25673/06_2025/7t4e_25673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4e_25673/06_2025/7t4e_25673.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4e_25673/06_2025/7t4e_25673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4e_25673/06_2025/7t4e_25673.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.90, per 1000 atoms: 0.56 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: 4.41 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.96 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: 6.70 Time building geometry restraints manager: 5.27 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: 0.02 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 43.960 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.280 ------------------------------------------------------------------------------- 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 : 10.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (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 TRP 0.019 0.001 TRP A 217 PHE 0.011 0.001 PHE F 100 TYR 0.016 0.001 TYR G 237 ARG 0.005 0.001 ARG H 225 Details of bonding type rmsd hydrogen bonds : bond 0.13833 ( 936) hydrogen bonds : angle 7.01634 ( 3267) covalent geometry : bond 0.00236 (19776) covalent geometry : angle 0.52513 (26808) *********************** 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 : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 ILE cc_start: 0.7926 (mm) cc_final: 0.7693 (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: 0.7618 (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: 0.6765 (m-30) cc_final: 0.6552 (m-30) REVERT: A 226 ASP cc_start: 0.6877 (t0) cc_final: 0.6537 (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: 0.6962 (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: 0.7002 (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: 0.6440 (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: 0.8414 (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: 0.6151 (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: 0.6962 (pm20) cc_final: 0.6562 (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: 1.5410 time to fit residues: 1407.1644 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 : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 0.0060 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.114829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.105521 restraints weight = 27989.875| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.94 r_work: 0.3297 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 19776 Z= 0.270 Angle : 0.579 9.269 26808 Z= 0.313 Chirality : 0.049 0.162 2936 Planarity : 0.006 0.050 3464 Dihedral : 4.709 17.990 2672 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.76 % Allowed : 12.78 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.17), residues: 2424 helix: -2.51 (0.42), residues: 96 sheet: 0.13 (0.14), residues: 1400 loop : -1.29 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 337 PHE 0.008 0.001 PHE B 333 TYR 0.034 0.002 TYR G 237 ARG 0.006 0.001 ARG E 135 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 936) hydrogen bonds : angle 5.20345 ( 3267) covalent geometry : bond 0.00580 (19776) covalent geometry : angle 0.57876 (26808) *********************** 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 837 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 799 time to evaluate : 2.125 Fit side-chains revert: symmetry clash REVERT: B 63 ASN cc_start: 0.8376 (t0) cc_final: 0.8105 (t0) REVERT: B 69 ASP cc_start: 0.7698 (m-30) cc_final: 0.7477 (m-30) REVERT: B 72 ASN cc_start: 0.8466 (m110) cc_final: 0.7886 (m110) REVERT: B 133 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8420 (ttmm) REVERT: B 160 GLU cc_start: 0.8127 (pm20) cc_final: 0.7786 (pm20) REVERT: B 164 SER cc_start: 0.8488 (t) cc_final: 0.8175 (p) REVERT: B 202 ASP cc_start: 0.7860 (m-30) cc_final: 0.7476 (m-30) REVERT: B 237 TYR cc_start: 0.8600 (m-80) cc_final: 0.8375 (m-10) REVERT: B 308 GLU cc_start: 0.7648 (pm20) cc_final: 0.7266 (pm20) REVERT: A 226 ASP cc_start: 0.7759 (t0) cc_final: 0.7337 (t0) REVERT: A 239 ASN cc_start: 0.8011 (t0) cc_final: 0.7809 (t0) REVERT: A 244 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7320 (ttp-170) REVERT: A 246 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7687 (tpp80) REVERT: A 258 LYS cc_start: 0.8945 (ptpp) cc_final: 0.8633 (ptpp) REVERT: A 308 GLU cc_start: 0.7778 (pm20) cc_final: 0.7454 (pm20) REVERT: A 321 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7871 (mmmt) REVERT: C 33 VAL cc_start: 0.8659 (p) cc_final: 0.8355 (t) REVERT: C 62 TYR cc_start: 0.8528 (m-80) cc_final: 0.8069 (m-80) REVERT: C 63 ASN cc_start: 0.8307 (t0) cc_final: 0.7922 (t0) REVERT: C 66 ASP cc_start: 0.8109 (t0) cc_final: 0.7901 (t0) REVERT: C 72 ASN cc_start: 0.8312 (m-40) cc_final: 0.7768 (m110) REVERT: C 187 GLU cc_start: 0.6863 (tp30) cc_final: 0.6610 (tp30) REVERT: C 202 ASP cc_start: 0.7803 (m-30) cc_final: 0.7474 (m-30) REVERT: C 223 GLU cc_start: 0.8112 (pt0) cc_final: 0.7875 (pt0) REVERT: C 246 ARG cc_start: 0.7837 (tpp80) cc_final: 0.7569 (tpp80) REVERT: C 308 GLU cc_start: 0.7762 (pm20) cc_final: 0.7357 (pm20) REVERT: C 330 ASP cc_start: 0.8021 (p0) cc_final: 0.7813 (p0) REVERT: D 41 GLU cc_start: 0.7970 (tt0) cc_final: 0.7739 (tt0) REVERT: D 159 LYS cc_start: 0.8565 (pttm) cc_final: 0.8253 (pttm) REVERT: D 218 ASP cc_start: 0.7794 (m-30) cc_final: 0.7362 (m-30) REVERT: D 246 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.7165 (ttm-80) REVERT: D 258 LYS cc_start: 0.8899 (ptpp) cc_final: 0.8635 (ptpp) REVERT: D 308 GLU cc_start: 0.7751 (pm20) cc_final: 0.7357 (pm20) REVERT: E 41 GLU cc_start: 0.7930 (tt0) cc_final: 0.7573 (tt0) REVERT: E 69 ASP cc_start: 0.7680 (m-30) cc_final: 0.7463 (m-30) REVERT: E 133 LYS cc_start: 0.8614 (tttm) cc_final: 0.8236 (tttm) REVERT: E 137 GLU cc_start: 0.7668 (mp0) cc_final: 0.7303 (mp0) REVERT: E 169 TYR cc_start: 0.7568 (m-80) cc_final: 0.7354 (m-10) REVERT: E 202 ASP cc_start: 0.7763 (m-30) cc_final: 0.7501 (m-30) REVERT: E 218 ASP cc_start: 0.7660 (m-30) cc_final: 0.7425 (m-30) REVERT: E 237 TYR cc_start: 0.8596 (m-80) cc_final: 0.8219 (m-10) REVERT: E 255 ASN cc_start: 0.8498 (t0) cc_final: 0.8163 (t0) REVERT: E 308 GLU cc_start: 0.7852 (pm20) cc_final: 0.7493 (pm20) REVERT: F 48 ILE cc_start: 0.8543 (mt) cc_final: 0.8289 (pp) REVERT: F 63 ASN cc_start: 0.8301 (t0) cc_final: 0.7988 (t0) REVERT: F 69 ASP cc_start: 0.7558 (m-30) cc_final: 0.7300 (m-30) REVERT: F 106 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7676 (ttp80) REVERT: F 137 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7917 (mt-10) REVERT: F 229 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8134 (m) REVERT: F 308 GLU cc_start: 0.7690 (pm20) cc_final: 0.7280 (pm20) REVERT: G 33 VAL cc_start: 0.8641 (p) cc_final: 0.8351 (t) REVERT: G 37 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7424 (mt-10) REVERT: G 63 ASN cc_start: 0.8316 (t0) cc_final: 0.8043 (t0) REVERT: G 106 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8178 (mtp180) REVERT: G 137 GLU cc_start: 0.7811 (mp0) cc_final: 0.7296 (mp0) REVERT: G 208 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8553 (pt) REVERT: G 241 MET cc_start: 0.8154 (mtm) cc_final: 0.7922 (mtp) REVERT: G 296 MET cc_start: 0.8242 (mpp) cc_final: 0.7771 (mpp) REVERT: G 308 GLU cc_start: 0.7721 (pm20) cc_final: 0.7285 (pm20) REVERT: G 329 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6896 (mt-10) REVERT: H 50 LYS cc_start: 0.8323 (tttp) cc_final: 0.7938 (tttm) REVERT: H 86 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8658 (mmtp) REVERT: H 226 ASP cc_start: 0.7771 (t70) cc_final: 0.7558 (t0) REVERT: H 231 ASN cc_start: 0.8417 (m110) cc_final: 0.8214 (m-40) REVERT: H 258 LYS cc_start: 0.8933 (ptpp) cc_final: 0.8597 (ptpp) REVERT: H 308 GLU cc_start: 0.7689 (pm20) cc_final: 0.7277 (pm20) outliers start: 38 outliers final: 10 residues processed: 808 average time/residue: 1.6449 time to fit residues: 1458.7552 Evaluate side-chains 790 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 773 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 244 ARG 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 106 ARG Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 86 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 12 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 121 optimal weight: 0.0470 chunk 169 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 233 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN C 316 ASN D 63 ASN D 231 ASN F 98 ASN H 63 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 = 0.3547 r_free = 0.3547 target = 0.115838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106421 restraints weight = 27708.608| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.95 r_work: 0.3308 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1910 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= 0.174 Angle : 0.536 8.704 26808 Z= 0.289 Chirality : 0.047 0.154 2936 Planarity : 0.005 0.060 3464 Dihedral : 4.511 16.438 2672 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.31 % Allowed : 14.95 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2424 helix: -2.42 (0.43), residues: 96 sheet: 0.06 (0.14), residues: 1400 loop : -1.36 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 PHE 0.009 0.001 PHE F 100 TYR 0.025 0.001 TYR G 237 ARG 0.009 0.001 ARG D 135 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 936) hydrogen bonds : angle 5.03270 ( 3267) covalent geometry : bond 0.00371 (19776) covalent geometry : angle 0.53585 (26808) *********************** 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 840 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 790 time to evaluate : 2.126 Fit side-chains revert: symmetry clash REVERT: B 69 ASP cc_start: 0.7722 (m-30) cc_final: 0.7466 (m-30) REVERT: B 75 SER cc_start: 0.8701 (t) cc_final: 0.8397 (p) REVERT: B 86 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8562 (mmtp) REVERT: B 108 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8475 (m) REVERT: B 132 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8248 (ttpt) REVERT: B 133 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8322 (ttmm) REVERT: B 160 GLU cc_start: 0.8109 (pm20) cc_final: 0.7733 (pm20) REVERT: B 202 ASP cc_start: 0.7850 (m-30) cc_final: 0.7455 (m-30) REVERT: B 237 TYR cc_start: 0.8651 (m-80) cc_final: 0.8448 (m-10) REVERT: B 308 GLU cc_start: 0.7595 (pm20) cc_final: 0.7188 (pm20) REVERT: A 133 LYS cc_start: 0.8692 (tttm) cc_final: 0.8437 (tttm) REVERT: A 159 LYS cc_start: 0.8486 (pttm) cc_final: 0.8104 (pttm) REVERT: A 226 ASP cc_start: 0.7752 (t0) cc_final: 0.7361 (t0) REVERT: A 244 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7473 (ttp-170) REVERT: A 246 ARG cc_start: 0.8121 (tpp80) cc_final: 0.7730 (mpp80) REVERT: A 258 LYS cc_start: 0.8935 (ptpp) cc_final: 0.8621 (ptpp) REVERT: A 274 MET cc_start: 0.8256 (mtp) cc_final: 0.7999 (mtp) REVERT: A 308 GLU cc_start: 0.7691 (pm20) cc_final: 0.7371 (pm20) REVERT: A 321 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7740 (mmmt) REVERT: C 33 VAL cc_start: 0.8669 (p) cc_final: 0.8373 (t) REVERT: C 62 TYR cc_start: 0.8519 (m-80) cc_final: 0.8103 (m-80) REVERT: C 63 ASN cc_start: 0.8283 (t0) cc_final: 0.7914 (t0) REVERT: C 72 ASN cc_start: 0.8298 (m-40) cc_final: 0.7631 (m110) REVERT: C 86 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8622 (mmtp) REVERT: C 187 GLU cc_start: 0.6876 (tp30) cc_final: 0.6596 (tp30) REVERT: C 202 ASP cc_start: 0.7746 (m-30) cc_final: 0.7419 (m-30) REVERT: C 255 ASN cc_start: 0.8537 (t0) cc_final: 0.8226 (t0) REVERT: C 296 MET cc_start: 0.8194 (mpp) cc_final: 0.7968 (mtm) REVERT: C 302 MET cc_start: 0.8324 (tpp) cc_final: 0.7998 (tpp) REVERT: C 308 GLU cc_start: 0.7749 (pm20) cc_final: 0.7332 (pm20) REVERT: C 330 ASP cc_start: 0.7969 (p0) cc_final: 0.7752 (p0) REVERT: D 41 GLU cc_start: 0.7943 (tt0) cc_final: 0.7716 (tt0) REVERT: D 132 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8137 (ttpt) REVERT: D 133 LYS cc_start: 0.8335 (tttm) cc_final: 0.8102 (tttm) REVERT: D 159 LYS cc_start: 0.8536 (pttm) cc_final: 0.8238 (pttm) REVERT: D 246 ARG cc_start: 0.7329 (ttm-80) cc_final: 0.7075 (ttm-80) REVERT: D 258 LYS cc_start: 0.8889 (ptpp) cc_final: 0.8640 (ptpp) REVERT: D 308 GLU cc_start: 0.7702 (pm20) cc_final: 0.7318 (pm20) REVERT: E 41 GLU cc_start: 0.7923 (tt0) cc_final: 0.7627 (tt0) REVERT: E 69 ASP cc_start: 0.7671 (m-30) cc_final: 0.7447 (m-30) REVERT: E 108 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8444 (t) REVERT: E 133 LYS cc_start: 0.8617 (tttm) cc_final: 0.8256 (tttm) REVERT: E 137 GLU cc_start: 0.7628 (mp0) cc_final: 0.7259 (mp0) REVERT: E 169 TYR cc_start: 0.7558 (m-80) cc_final: 0.7337 (m-10) REVERT: E 202 ASP cc_start: 0.7758 (m-30) cc_final: 0.7422 (m-30) REVERT: E 218 ASP cc_start: 0.7607 (m-30) cc_final: 0.7334 (m-30) REVERT: E 237 TYR cc_start: 0.8581 (m-80) cc_final: 0.8295 (m-10) REVERT: E 258 LYS cc_start: 0.9010 (ptpp) cc_final: 0.8734 (ptpp) REVERT: E 308 GLU cc_start: 0.7784 (pm20) cc_final: 0.7430 (pm20) REVERT: F 63 ASN cc_start: 0.8252 (t0) cc_final: 0.8009 (t0) REVERT: F 69 ASP cc_start: 0.7530 (m-30) cc_final: 0.7292 (m-30) REVERT: F 137 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7916 (mt-10) REVERT: F 229 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8141 (m) REVERT: F 244 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7730 (ttp-170) REVERT: F 246 ARG cc_start: 0.7954 (tpp80) cc_final: 0.7688 (tpp80) REVERT: F 308 GLU cc_start: 0.7634 (pm20) cc_final: 0.7258 (pm20) REVERT: G 33 VAL cc_start: 0.8685 (p) cc_final: 0.8389 (t) REVERT: G 37 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7399 (mt-10) REVERT: G 63 ASN cc_start: 0.8292 (t0) cc_final: 0.8010 (t0) REVERT: G 70 THR cc_start: 0.8312 (p) cc_final: 0.8059 (p) REVERT: G 75 SER cc_start: 0.8655 (t) cc_final: 0.8377 (p) REVERT: G 106 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8132 (mtp180) REVERT: G 133 LYS cc_start: 0.8728 (tttm) cc_final: 0.8106 (tttm) REVERT: G 137 GLU cc_start: 0.7748 (mp0) cc_final: 0.7269 (mp0) REVERT: G 208 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8500 (pt) REVERT: G 209 LYS cc_start: 0.8809 (tttm) cc_final: 0.8603 (ttmm) REVERT: G 296 MET cc_start: 0.8293 (mpp) cc_final: 0.7584 (mpp) REVERT: G 308 GLU cc_start: 0.7638 (pm20) cc_final: 0.7210 (pm20) REVERT: G 329 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6759 (mt-10) REVERT: H 50 LYS cc_start: 0.8304 (tttp) cc_final: 0.7783 (tttm) REVERT: H 86 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8636 (mmtp) REVERT: H 91 MET cc_start: 0.8477 (mtm) cc_final: 0.8245 (mtp) REVERT: H 159 LYS cc_start: 0.8485 (pttm) cc_final: 0.7920 (pttm) REVERT: H 226 ASP cc_start: 0.7682 (t70) cc_final: 0.7423 (t0) REVERT: H 258 LYS cc_start: 0.8930 (ptpp) cc_final: 0.8590 (ptpp) REVERT: H 308 GLU cc_start: 0.7645 (pm20) cc_final: 0.7274 (pm20) outliers start: 50 outliers final: 16 residues processed: 804 average time/residue: 1.6672 time to fit residues: 1469.2069 Evaluate side-chains 802 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 774 time to evaluate : 2.579 ------------------------------------------------------------------------------- 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 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 49 VAL 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 108 VAL 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 229 THR Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 229 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 39 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 89 optimal weight: 0.0980 chunk 158 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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** A 316 ASN C 231 ASN D 239 ASN E 231 ASN H 63 ASN H 316 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105188 restraints weight = 28048.513| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.95 r_work: 0.3286 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19776 Z= 0.244 Angle : 0.563 8.149 26808 Z= 0.303 Chirality : 0.048 0.161 2936 Planarity : 0.006 0.062 3464 Dihedral : 4.668 17.984 2672 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.78 % Allowed : 16.99 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.17), residues: 2424 helix: -2.31 (0.44), residues: 96 sheet: 0.03 (0.14), residues: 1384 loop : -1.46 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 337 PHE 0.010 0.001 PHE B 333 TYR 0.028 0.001 TYR G 237 ARG 0.012 0.001 ARG D 135 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 936) hydrogen bonds : angle 4.96788 ( 3267) covalent geometry : bond 0.00522 (19776) covalent geometry : angle 0.56315 (26808) *********************** 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 841 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 781 time to evaluate : 2.227 Fit side-chains revert: symmetry clash REVERT: B 62 TYR cc_start: 0.8668 (m-80) cc_final: 0.7777 (m-80) REVERT: B 69 ASP cc_start: 0.7681 (m-30) cc_final: 0.7442 (m-30) REVERT: B 75 SER cc_start: 0.8715 (t) cc_final: 0.8399 (p) REVERT: B 133 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8305 (ttmm) REVERT: B 202 ASP cc_start: 0.7875 (m-30) cc_final: 0.7477 (m-30) REVERT: B 308 GLU cc_start: 0.7635 (pm20) cc_final: 0.7169 (pm20) REVERT: A 159 LYS cc_start: 0.8510 (pttm) cc_final: 0.8087 (pttm) REVERT: A 226 ASP cc_start: 0.7775 (t0) cc_final: 0.7347 (t0) REVERT: A 246 ARG cc_start: 0.8142 (tpp80) cc_final: 0.7755 (mpp80) REVERT: A 258 LYS cc_start: 0.8929 (ptpp) cc_final: 0.8717 (ptpp) REVERT: A 308 GLU cc_start: 0.7740 (pm20) cc_final: 0.7406 (pm20) REVERT: A 321 LYS cc_start: 0.8022 (mtmt) cc_final: 0.7766 (mmmt) REVERT: C 66 ASP cc_start: 0.8028 (t0) cc_final: 0.7710 (t0) REVERT: C 72 ASN cc_start: 0.8267 (m-40) cc_final: 0.8001 (m110) REVERT: C 86 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8641 (mmtp) REVERT: C 112 LYS cc_start: 0.7864 (mttp) cc_final: 0.7653 (mttp) REVERT: C 187 GLU cc_start: 0.6923 (tp30) cc_final: 0.6645 (tp30) REVERT: C 202 ASP cc_start: 0.7744 (m-30) cc_final: 0.7419 (m-30) REVERT: C 203 TYR cc_start: 0.8840 (m-80) cc_final: 0.8618 (m-80) REVERT: C 226 ASP cc_start: 0.7915 (t70) cc_final: 0.7638 (t70) REVERT: C 246 ARG cc_start: 0.7958 (tpp80) cc_final: 0.7748 (mpp80) REVERT: C 302 MET cc_start: 0.8400 (tpp) cc_final: 0.8049 (tpp) REVERT: C 308 GLU cc_start: 0.7798 (pm20) cc_final: 0.7375 (pm20) REVERT: C 322 GLU cc_start: 0.8355 (pt0) cc_final: 0.8085 (pt0) REVERT: C 330 ASP cc_start: 0.7997 (p0) cc_final: 0.7791 (p0) REVERT: D 41 GLU cc_start: 0.7966 (tt0) cc_final: 0.7742 (tt0) REVERT: D 135 ARG cc_start: 0.8408 (ttm-80) cc_final: 0.8116 (ttm-80) REVERT: D 159 LYS cc_start: 0.8597 (pttm) cc_final: 0.8300 (pttm) REVERT: D 246 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7353 (ttm-80) REVERT: D 258 LYS cc_start: 0.8869 (ptpp) cc_final: 0.8626 (ptpp) REVERT: D 308 GLU cc_start: 0.7760 (pm20) cc_final: 0.7379 (pm20) REVERT: E 41 GLU cc_start: 0.7912 (tt0) cc_final: 0.7629 (tt0) REVERT: E 69 ASP cc_start: 0.7668 (m-30) cc_final: 0.7442 (m-30) REVERT: E 133 LYS cc_start: 0.8567 (tttm) cc_final: 0.8137 (tttm) REVERT: E 137 GLU cc_start: 0.7752 (mp0) cc_final: 0.7412 (mp0) REVERT: E 169 TYR cc_start: 0.7568 (m-80) cc_final: 0.7363 (m-10) REVERT: E 202 ASP cc_start: 0.7789 (m-30) cc_final: 0.7517 (m-30) REVERT: E 218 ASP cc_start: 0.7631 (m-30) cc_final: 0.7337 (m-30) REVERT: E 237 TYR cc_start: 0.8629 (m-80) cc_final: 0.8402 (m-10) REVERT: E 258 LYS cc_start: 0.9013 (ptpp) cc_final: 0.8741 (ptpp) REVERT: E 308 GLU cc_start: 0.7869 (pm20) cc_final: 0.7505 (pm20) REVERT: E 329 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7292 (mt-10) REVERT: F 50 LYS cc_start: 0.8256 (tttt) cc_final: 0.7973 (tttm) REVERT: F 69 ASP cc_start: 0.7520 (m-30) cc_final: 0.7287 (m-30) REVERT: F 137 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7900 (mt-10) REVERT: F 210 LYS cc_start: 0.8730 (tmtt) cc_final: 0.8510 (tmtt) REVERT: F 229 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8164 (m) REVERT: F 244 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7682 (ttp-170) REVERT: F 246 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7618 (tpp80) REVERT: F 282 ASN cc_start: 0.8036 (m-40) cc_final: 0.7813 (m-40) REVERT: F 308 GLU cc_start: 0.7725 (pm20) cc_final: 0.7361 (pm20) REVERT: G 33 VAL cc_start: 0.8664 (p) cc_final: 0.8359 (t) REVERT: G 37 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7435 (mt-10) REVERT: G 63 ASN cc_start: 0.8344 (t0) cc_final: 0.8095 (t0) REVERT: G 75 SER cc_start: 0.8677 (t) cc_final: 0.8371 (p) REVERT: G 90 GLU cc_start: 0.7648 (pm20) cc_final: 0.7294 (pm20) REVERT: G 133 LYS cc_start: 0.8694 (tttm) cc_final: 0.8270 (tttp) REVERT: G 137 GLU cc_start: 0.7833 (mp0) cc_final: 0.7611 (mt-10) REVERT: G 296 MET cc_start: 0.8288 (mpp) cc_final: 0.7776 (mpp) REVERT: G 308 GLU cc_start: 0.7612 (pm20) cc_final: 0.7167 (pm20) REVERT: G 329 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6919 (mt-10) REVERT: H 50 LYS cc_start: 0.8337 (tttp) cc_final: 0.8044 (tttm) REVERT: H 135 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8113 (ttp-170) REVERT: H 159 LYS cc_start: 0.8465 (pttm) cc_final: 0.7809 (pttm) REVERT: H 226 ASP cc_start: 0.7797 (t70) cc_final: 0.7471 (t0) REVERT: H 258 LYS cc_start: 0.8908 (ptpp) cc_final: 0.8580 (ptpp) REVERT: H 308 GLU cc_start: 0.7697 (pm20) cc_final: 0.7362 (pm20) outliers start: 60 outliers final: 25 residues processed: 795 average time/residue: 1.7421 time to fit residues: 1514.6728 Evaluate side-chains 803 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 773 time to evaluate : 2.991 ------------------------------------------------------------------------------- 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 296 MET Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 86 LYS 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 236 VAL Chi-restraints excluded: chain E residue 36 THR 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 229 THR Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 TYR Chi-restraints excluded: chain H residue 208 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 195 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 64 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 234 optimal weight: 9.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN C 231 ASN E 231 ASN F 231 ASN F 316 ASN G 316 ASN H 63 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.113115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.103940 restraints weight = 28179.629| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.94 r_work: 0.3266 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 19776 Z= 0.329 Angle : 0.601 8.109 26808 Z= 0.324 Chirality : 0.049 0.172 2936 Planarity : 0.006 0.067 3464 Dihedral : 4.930 23.036 2672 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.50 % Allowed : 18.52 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2424 helix: -4.05 (0.24), residues: 48 sheet: 0.09 (0.14), residues: 1360 loop : -1.24 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 337 PHE 0.011 0.001 PHE B 333 TYR 0.033 0.002 TYR G 237 ARG 0.011 0.001 ARG D 135 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 936) hydrogen bonds : angle 5.07513 ( 3267) covalent geometry : bond 0.00708 (19776) covalent geometry : angle 0.60147 (26808) *********************** 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 837 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 783 time to evaluate : 3.392 Fit side-chains revert: symmetry clash REVERT: B 69 ASP cc_start: 0.7706 (m-30) cc_final: 0.7482 (m-30) REVERT: B 202 ASP cc_start: 0.7905 (m-30) cc_final: 0.7510 (m-30) REVERT: B 258 LYS cc_start: 0.8963 (ptpp) cc_final: 0.8742 (ptpp) REVERT: B 308 GLU cc_start: 0.7702 (pm20) cc_final: 0.7331 (pm20) REVERT: A 159 LYS cc_start: 0.8548 (pttm) cc_final: 0.8113 (pttm) REVERT: A 226 ASP cc_start: 0.7854 (t0) cc_final: 0.7393 (t0) REVERT: A 308 GLU cc_start: 0.7816 (pm20) cc_final: 0.7504 (pm20) REVERT: A 321 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7838 (mmmt) REVERT: A 340 ARG cc_start: 0.8824 (mtm-85) cc_final: 0.8583 (mpp-170) REVERT: C 66 ASP cc_start: 0.8090 (t0) cc_final: 0.7825 (t0) REVERT: C 72 ASN cc_start: 0.8286 (m-40) cc_final: 0.7939 (m110) REVERT: C 112 LYS cc_start: 0.7886 (mttp) cc_final: 0.7608 (mttp) REVERT: C 187 GLU cc_start: 0.6950 (tp30) cc_final: 0.6639 (tp30) REVERT: C 202 ASP cc_start: 0.7769 (m-30) cc_final: 0.7475 (m-30) REVERT: C 226 ASP cc_start: 0.7906 (t70) cc_final: 0.7624 (t70) REVERT: C 258 LYS cc_start: 0.8942 (ptpp) cc_final: 0.8691 (ptpp) REVERT: C 296 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7940 (mtm) REVERT: C 308 GLU cc_start: 0.7867 (pm20) cc_final: 0.7490 (pm20) REVERT: C 330 ASP cc_start: 0.8040 (p0) cc_final: 0.7821 (p0) REVERT: D 41 GLU cc_start: 0.8001 (tt0) cc_final: 0.7790 (tt0) REVERT: D 159 LYS cc_start: 0.8625 (pttm) cc_final: 0.8283 (pttm) REVERT: D 308 GLU cc_start: 0.7844 (pm20) cc_final: 0.7524 (pm20) REVERT: D 321 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7995 (mtpp) REVERT: E 41 GLU cc_start: 0.7903 (tt0) cc_final: 0.7625 (tt0) REVERT: E 69 ASP cc_start: 0.7671 (m-30) cc_final: 0.7453 (m-30) REVERT: E 133 LYS cc_start: 0.8560 (tttm) cc_final: 0.8121 (tttm) REVERT: E 202 ASP cc_start: 0.7790 (m-30) cc_final: 0.7517 (m-30) REVERT: E 218 ASP cc_start: 0.7732 (m-30) cc_final: 0.7357 (m-30) REVERT: E 237 TYR cc_start: 0.8694 (m-80) cc_final: 0.8321 (m-10) REVERT: E 274 MET cc_start: 0.8463 (mtp) cc_final: 0.8212 (mtp) REVERT: E 302 MET cc_start: 0.8500 (tpp) cc_final: 0.7995 (tpp) REVERT: E 308 GLU cc_start: 0.7884 (pm20) cc_final: 0.7541 (pm20) REVERT: F 49 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8620 (m) REVERT: F 50 LYS cc_start: 0.8324 (tttt) cc_final: 0.8109 (tttm) REVERT: F 69 ASP cc_start: 0.7552 (m-30) cc_final: 0.7314 (m-30) REVERT: F 229 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8208 (m) REVERT: F 244 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7833 (ttp-170) REVERT: F 246 ARG cc_start: 0.8222 (tpp80) cc_final: 0.7686 (mpp80) REVERT: F 308 GLU cc_start: 0.7866 (pm20) cc_final: 0.7510 (pm20) REVERT: G 37 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7427 (mt-10) REVERT: G 90 GLU cc_start: 0.7633 (pm20) cc_final: 0.7278 (pm20) REVERT: G 133 LYS cc_start: 0.8729 (tttm) cc_final: 0.8508 (tttp) REVERT: G 135 ARG cc_start: 0.8485 (tpp80) cc_final: 0.8285 (tpp80) REVERT: G 137 GLU cc_start: 0.7848 (mp0) cc_final: 0.7626 (mt-10) REVERT: G 329 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7034 (mt-10) REVERT: H 50 LYS cc_start: 0.8382 (tttp) cc_final: 0.8062 (tttm) REVERT: H 135 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8097 (ttp-170) REVERT: H 159 LYS cc_start: 0.8496 (pttm) cc_final: 0.7876 (pttm) REVERT: H 293 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8396 (m) REVERT: H 308 GLU cc_start: 0.7808 (pm20) cc_final: 0.7441 (pm20) REVERT: H 329 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7163 (mt-10) outliers start: 54 outliers final: 24 residues processed: 800 average time/residue: 1.7792 time to fit residues: 1557.9897 Evaluate side-chains 812 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 782 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain A residue 169 TYR 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 C residue 280 SER Chi-restraints excluded: chain C residue 296 MET 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 226 ASP 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 197 THR Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 202 ASP 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 293 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 5 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 171 optimal weight: 0.0870 chunk 230 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN C 145 GLN D 98 ASN E 231 ASN E 316 ASN F 231 ASN G 63 ASN H 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105623 restraints weight = 27835.331| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.95 r_work: 0.3302 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19776 Z= 0.182 Angle : 0.551 7.660 26808 Z= 0.299 Chirality : 0.048 0.162 2936 Planarity : 0.005 0.065 3464 Dihedral : 4.674 18.810 2672 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.45 % Allowed : 20.14 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.17), residues: 2424 helix: -2.30 (0.44), residues: 96 sheet: -0.04 (0.14), residues: 1384 loop : -1.41 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 217 PHE 0.008 0.001 PHE B 333 TYR 0.027 0.001 TYR B 237 ARG 0.006 0.001 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 936) hydrogen bonds : angle 4.90057 ( 3267) covalent geometry : bond 0.00387 (19776) covalent geometry : angle 0.55108 (26808) *********************** 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 848 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 795 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.7603 (m-30) cc_final: 0.7380 (m-30) REVERT: B 75 SER cc_start: 0.8720 (t) cc_final: 0.8414 (p) REVERT: B 167 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8249 (tp) REVERT: B 202 ASP cc_start: 0.7976 (m-30) cc_final: 0.7610 (m-30) REVERT: B 258 LYS cc_start: 0.8930 (ptpp) cc_final: 0.8728 (ptpp) REVERT: B 308 GLU cc_start: 0.7712 (pm20) cc_final: 0.7324 (pm20) REVERT: A 159 LYS cc_start: 0.8524 (pttm) cc_final: 0.8111 (pttm) REVERT: A 226 ASP cc_start: 0.7791 (t0) cc_final: 0.7321 (t0) REVERT: A 308 GLU cc_start: 0.7760 (pm20) cc_final: 0.7447 (pm20) REVERT: A 321 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7753 (mmmt) REVERT: C 66 ASP cc_start: 0.8017 (t0) cc_final: 0.7694 (t0) REVERT: C 72 ASN cc_start: 0.8209 (m-40) cc_final: 0.7503 (m-40) REVERT: C 187 GLU cc_start: 0.7027 (tp30) cc_final: 0.6736 (tp30) REVERT: C 202 ASP cc_start: 0.7862 (m-30) cc_final: 0.7567 (m-30) REVERT: C 258 LYS cc_start: 0.8884 (ptpp) cc_final: 0.8651 (ptpp) REVERT: C 296 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7758 (mtm) REVERT: C 308 GLU cc_start: 0.7881 (pm20) cc_final: 0.7449 (pm20) REVERT: C 322 GLU cc_start: 0.8328 (pt0) cc_final: 0.8069 (pt0) REVERT: C 329 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6727 (mt-10) REVERT: C 330 ASP cc_start: 0.8004 (p0) cc_final: 0.7792 (p0) REVERT: D 41 GLU cc_start: 0.7967 (tt0) cc_final: 0.7767 (tt0) REVERT: D 159 LYS cc_start: 0.8573 (pttm) cc_final: 0.8249 (pttm) REVERT: D 308 GLU cc_start: 0.7801 (pm20) cc_final: 0.7468 (pm20) REVERT: D 321 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7808 (mtpp) REVERT: E 37 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: E 41 GLU cc_start: 0.7940 (tt0) cc_final: 0.7684 (tt0) REVERT: E 62 TYR cc_start: 0.8551 (m-80) cc_final: 0.7752 (m-80) REVERT: E 133 LYS cc_start: 0.8531 (tttm) cc_final: 0.7996 (tttm) REVERT: E 137 GLU cc_start: 0.7711 (mp0) cc_final: 0.7344 (mp0) REVERT: E 202 ASP cc_start: 0.7863 (m-30) cc_final: 0.7500 (m-30) REVERT: E 203 TYR cc_start: 0.8830 (m-80) cc_final: 0.8609 (m-80) REVERT: E 218 ASP cc_start: 0.7696 (m-30) cc_final: 0.7356 (m-30) REVERT: E 237 TYR cc_start: 0.8640 (m-80) cc_final: 0.8371 (m-80) REVERT: E 274 MET cc_start: 0.8374 (mtp) cc_final: 0.8110 (mtp) REVERT: E 296 MET cc_start: 0.8278 (mpp) cc_final: 0.7778 (mpp) REVERT: E 308 GLU cc_start: 0.7864 (pm20) cc_final: 0.7520 (pm20) REVERT: E 329 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7242 (mt-10) REVERT: F 69 ASP cc_start: 0.7474 (m-30) cc_final: 0.7246 (m-30) REVERT: F 132 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8369 (ttmt) REVERT: F 137 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7903 (mt-10) REVERT: F 229 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8112 (m) REVERT: F 246 ARG cc_start: 0.8173 (tpp80) cc_final: 0.7743 (mpp80) REVERT: F 308 GLU cc_start: 0.7724 (pm20) cc_final: 0.7375 (pm20) REVERT: G 33 VAL cc_start: 0.8667 (p) cc_final: 0.8358 (t) REVERT: G 37 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7272 (mt-10) REVERT: G 75 SER cc_start: 0.8670 (t) cc_final: 0.8383 (p) REVERT: G 90 GLU cc_start: 0.7500 (pm20) cc_final: 0.7157 (pm20) REVERT: G 133 LYS cc_start: 0.8638 (tttm) cc_final: 0.8400 (tttp) REVERT: G 135 ARG cc_start: 0.8446 (tpp80) cc_final: 0.8234 (tpp80) REVERT: G 329 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6996 (mt-10) REVERT: H 50 LYS cc_start: 0.8303 (tttp) cc_final: 0.7690 (tttm) REVERT: H 135 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8095 (ttp-170) REVERT: H 159 LYS cc_start: 0.8527 (pttm) cc_final: 0.8031 (pttm) REVERT: H 308 GLU cc_start: 0.7770 (pm20) cc_final: 0.7423 (pm20) REVERT: H 329 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6792 (mt-10) outliers start: 53 outliers final: 23 residues processed: 811 average time/residue: 2.0924 time to fit residues: 1867.1905 Evaluate side-chains 805 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 777 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 296 MET 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 226 ASP Chi-restraints excluded: chain E residue 37 GLU 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 96 SER 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 F residue 274 MET Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 52 ILE 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 135 ARG 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 160 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 165 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 184 optimal weight: 0.2980 chunk 132 optimal weight: 0.0770 chunk 219 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 GLN C 231 ASN E 231 ASN F 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 = 0.3537 r_free = 0.3537 target = 0.115643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106649 restraints weight = 27760.035| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.92 r_work: 0.3314 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2442 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= 0.160 Angle : 0.551 7.611 26808 Z= 0.298 Chirality : 0.047 0.159 2936 Planarity : 0.005 0.063 3464 Dihedral : 4.561 17.251 2672 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.31 % Allowed : 21.11 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.17), residues: 2424 helix: -2.30 (0.44), residues: 96 sheet: 0.04 (0.14), residues: 1400 loop : -1.49 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 217 PHE 0.009 0.001 PHE D 100 TYR 0.019 0.001 TYR G 237 ARG 0.007 0.001 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 936) hydrogen bonds : angle 4.81071 ( 3267) covalent geometry : bond 0.00343 (19776) covalent geometry : angle 0.55052 (26808) *********************** 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 847 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 797 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.7629 (m-30) cc_final: 0.7389 (m-30) REVERT: B 75 SER cc_start: 0.8710 (t) cc_final: 0.8393 (p) REVERT: B 167 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8250 (tp) REVERT: B 202 ASP cc_start: 0.8002 (m-30) cc_final: 0.7655 (m-30) REVERT: B 258 LYS cc_start: 0.8907 (ptpp) cc_final: 0.8611 (ptpp) REVERT: B 308 GLU cc_start: 0.7740 (pm20) cc_final: 0.7345 (pm20) REVERT: A 159 LYS cc_start: 0.8450 (pttm) cc_final: 0.8016 (pttm) REVERT: A 226 ASP cc_start: 0.7776 (t0) cc_final: 0.7333 (t0) REVERT: A 308 GLU cc_start: 0.7745 (pm20) cc_final: 0.7437 (pm20) REVERT: A 321 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7745 (mmmt) REVERT: C 33 VAL cc_start: 0.8708 (p) cc_final: 0.8399 (t) REVERT: C 66 ASP cc_start: 0.8102 (t0) cc_final: 0.7764 (t0) REVERT: C 72 ASN cc_start: 0.8211 (m-40) cc_final: 0.7475 (m-40) REVERT: C 107 TYR cc_start: 0.8579 (m-80) cc_final: 0.8344 (m-80) REVERT: C 187 GLU cc_start: 0.7006 (tp30) cc_final: 0.6720 (tp30) REVERT: C 202 ASP cc_start: 0.7854 (m-30) cc_final: 0.7553 (m-30) REVERT: C 226 ASP cc_start: 0.7946 (t70) cc_final: 0.7652 (t70) REVERT: C 258 LYS cc_start: 0.8860 (ptpp) cc_final: 0.8531 (ptpp) REVERT: C 296 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7665 (mtm) REVERT: C 303 ARG cc_start: 0.8674 (mtt90) cc_final: 0.8395 (mtt180) REVERT: C 308 GLU cc_start: 0.7821 (pm20) cc_final: 0.7378 (pm20) REVERT: C 322 GLU cc_start: 0.8294 (pt0) cc_final: 0.8055 (pt0) REVERT: C 329 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6641 (mt-10) REVERT: C 330 ASP cc_start: 0.7961 (p0) cc_final: 0.7734 (p0) REVERT: D 41 GLU cc_start: 0.7949 (tt0) cc_final: 0.7738 (tt0) REVERT: D 159 LYS cc_start: 0.8576 (pttm) cc_final: 0.8236 (pttm) REVERT: D 308 GLU cc_start: 0.7754 (pm20) cc_final: 0.7425 (pm20) REVERT: D 321 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7858 (mtpp) REVERT: E 37 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: E 41 GLU cc_start: 0.7957 (tt0) cc_final: 0.7689 (tt0) REVERT: E 133 LYS cc_start: 0.8506 (tttm) cc_final: 0.8015 (tttm) REVERT: E 137 GLU cc_start: 0.7736 (mp0) cc_final: 0.7371 (mp0) REVERT: E 202 ASP cc_start: 0.7900 (m-30) cc_final: 0.7533 (m-30) REVERT: E 203 TYR cc_start: 0.8813 (m-80) cc_final: 0.8582 (m-80) REVERT: E 218 ASP cc_start: 0.7677 (m-30) cc_final: 0.7318 (m-30) REVERT: E 228 TYR cc_start: 0.8684 (m-80) cc_final: 0.8453 (m-80) REVERT: E 231 ASN cc_start: 0.8437 (m110) cc_final: 0.8192 (m-40) REVERT: E 237 TYR cc_start: 0.8611 (m-80) cc_final: 0.8312 (m-10) REVERT: E 274 MET cc_start: 0.8336 (mtp) cc_final: 0.8111 (mtp) REVERT: E 308 GLU cc_start: 0.7890 (pm20) cc_final: 0.7542 (pm20) REVERT: E 329 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7245 (mt-10) REVERT: E 330 ASP cc_start: 0.7954 (p0) cc_final: 0.7740 (p0) REVERT: F 69 ASP cc_start: 0.7489 (m-30) cc_final: 0.7260 (m-30) REVERT: F 132 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8321 (ttmt) REVERT: F 229 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8072 (m) REVERT: F 246 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7660 (mpp80) REVERT: F 308 GLU cc_start: 0.7746 (pm20) cc_final: 0.7396 (pm20) REVERT: G 33 VAL cc_start: 0.8689 (p) cc_final: 0.8379 (t) REVERT: G 37 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7425 (mt-10) REVERT: G 75 SER cc_start: 0.8643 (t) cc_final: 0.8355 (p) REVERT: G 90 GLU cc_start: 0.7467 (pm20) cc_final: 0.7129 (pm20) REVERT: G 133 LYS cc_start: 0.8626 (tttm) cc_final: 0.8399 (tttp) REVERT: G 135 ARG cc_start: 0.8424 (tpp80) cc_final: 0.8218 (tpp80) REVERT: G 329 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6940 (mt-10) REVERT: G 340 ARG cc_start: 0.8669 (mmt90) cc_final: 0.8463 (mpt-90) REVERT: H 50 LYS cc_start: 0.8269 (tttp) cc_final: 0.8066 (tttm) REVERT: H 86 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8526 (mmtp) REVERT: H 90 GLU cc_start: 0.7402 (pm20) cc_final: 0.6965 (pm20) REVERT: H 135 ARG cc_start: 0.8359 (tpp80) cc_final: 0.7940 (ttp-170) REVERT: H 159 LYS cc_start: 0.8505 (pttm) cc_final: 0.8078 (pttm) REVERT: H 208 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8443 (pt) REVERT: H 308 GLU cc_start: 0.7747 (pm20) cc_final: 0.7409 (pm20) REVERT: H 329 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6711 (mt-10) outliers start: 50 outliers final: 23 residues processed: 810 average time/residue: 1.7054 time to fit residues: 1509.1232 Evaluate side-chains 812 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 783 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain D 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 37 GLU Chi-restraints excluded: chain E residue 128 MET 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 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 F residue 274 MET Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 222 VAL 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 215 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN D 72 ASN E 63 ASN F 231 ASN F 282 ASN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.104850 restraints weight = 27915.139| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.91 r_work: 0.3288 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 19776 Z= 0.277 Angle : 0.602 8.020 26808 Z= 0.324 Chirality : 0.049 0.167 2936 Planarity : 0.006 0.063 3464 Dihedral : 4.835 21.721 2672 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.27 % Allowed : 21.44 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2424 helix: -3.91 (0.27), residues: 48 sheet: -0.02 (0.14), residues: 1384 loop : -1.07 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 337 PHE 0.010 0.001 PHE B 333 TYR 0.034 0.002 TYR F 237 ARG 0.013 0.001 ARG B 246 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 936) hydrogen bonds : angle 4.94562 ( 3267) covalent geometry : bond 0.00597 (19776) covalent geometry : angle 0.60224 (26808) *********************** 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 831 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 782 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.7620 (m-30) cc_final: 0.7396 (m-30) REVERT: B 75 SER cc_start: 0.8684 (t) cc_final: 0.8368 (p) REVERT: B 202 ASP cc_start: 0.8023 (m-30) cc_final: 0.7665 (m-30) REVERT: B 258 LYS cc_start: 0.8919 (ptpp) cc_final: 0.8689 (ptpp) REVERT: B 308 GLU cc_start: 0.7822 (pm20) cc_final: 0.7430 (pm20) REVERT: A 39 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8266 (m) REVERT: A 159 LYS cc_start: 0.8486 (pttm) cc_final: 0.8024 (pttm) REVERT: A 226 ASP cc_start: 0.7830 (t0) cc_final: 0.7362 (t0) REVERT: A 308 GLU cc_start: 0.7784 (pm20) cc_final: 0.7467 (pm20) REVERT: A 321 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7823 (mmmt) REVERT: C 66 ASP cc_start: 0.8125 (t0) cc_final: 0.7769 (t0) REVERT: C 72 ASN cc_start: 0.8198 (m-40) cc_final: 0.7940 (m-40) REVERT: C 202 ASP cc_start: 0.7866 (m-30) cc_final: 0.7570 (m-30) REVERT: C 258 LYS cc_start: 0.8859 (ptpp) cc_final: 0.8607 (ptpp) REVERT: C 308 GLU cc_start: 0.7868 (pm20) cc_final: 0.7473 (pm20) REVERT: C 322 GLU cc_start: 0.8352 (pt0) cc_final: 0.8096 (pt0) REVERT: C 330 ASP cc_start: 0.8012 (p0) cc_final: 0.7787 (p0) REVERT: D 41 GLU cc_start: 0.7985 (tt0) cc_final: 0.7768 (tt0) REVERT: D 132 LYS cc_start: 0.8487 (ttpt) cc_final: 0.8172 (ttpt) REVERT: D 159 LYS cc_start: 0.8615 (pttm) cc_final: 0.8265 (pttm) REVERT: D 274 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7955 (mtp) REVERT: D 308 GLU cc_start: 0.7847 (pm20) cc_final: 0.7520 (pm20) REVERT: D 321 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7908 (mtpp) REVERT: E 37 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: E 41 GLU cc_start: 0.7893 (tt0) cc_final: 0.7647 (tt0) REVERT: E 72 ASN cc_start: 0.8365 (m110) cc_final: 0.8162 (m110) REVERT: E 133 LYS cc_start: 0.8528 (tttm) cc_final: 0.7982 (tttm) REVERT: E 137 GLU cc_start: 0.7750 (mp0) cc_final: 0.7395 (mp0) REVERT: E 202 ASP cc_start: 0.7876 (m-30) cc_final: 0.7586 (m-30) REVERT: E 218 ASP cc_start: 0.7705 (m-30) cc_final: 0.7339 (m-30) REVERT: E 237 TYR cc_start: 0.8705 (m-80) cc_final: 0.8355 (m-10) REVERT: E 296 MET cc_start: 0.8193 (mpp) cc_final: 0.7678 (mpp) REVERT: E 308 GLU cc_start: 0.7935 (pm20) cc_final: 0.7591 (pm20) REVERT: E 330 ASP cc_start: 0.7995 (p0) cc_final: 0.7791 (p0) REVERT: F 49 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8638 (m) REVERT: F 50 LYS cc_start: 0.8332 (tttt) cc_final: 0.7555 (tttm) REVERT: F 69 ASP cc_start: 0.7554 (m-30) cc_final: 0.7304 (m-30) REVERT: F 167 ILE cc_start: 0.8467 (mp) cc_final: 0.8122 (mp) REVERT: F 229 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8127 (m) REVERT: F 246 ARG cc_start: 0.8090 (tpp80) cc_final: 0.7763 (mpp80) REVERT: F 308 GLU cc_start: 0.7843 (pm20) cc_final: 0.7473 (pm20) REVERT: F 329 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7026 (mt-10) REVERT: G 37 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7401 (mt-10) REVERT: G 75 SER cc_start: 0.8638 (t) cc_final: 0.8380 (p) REVERT: G 90 GLU cc_start: 0.7474 (pm20) cc_final: 0.7106 (pm20) REVERT: G 133 LYS cc_start: 0.8608 (tttm) cc_final: 0.8385 (tttp) REVERT: G 135 ARG cc_start: 0.8475 (tpp80) cc_final: 0.8187 (tpp80) REVERT: G 258 LYS cc_start: 0.8939 (ptpp) cc_final: 0.8660 (pttm) REVERT: G 308 GLU cc_start: 0.7758 (pm20) cc_final: 0.7297 (pm20) REVERT: G 329 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7000 (mt-10) REVERT: H 50 LYS cc_start: 0.8352 (tttp) cc_final: 0.7980 (tttm) REVERT: H 90 GLU cc_start: 0.7400 (pm20) cc_final: 0.6941 (pm20) REVERT: H 135 ARG cc_start: 0.8438 (tpp80) cc_final: 0.8109 (ttp-170) REVERT: H 159 LYS cc_start: 0.8563 (pttm) cc_final: 0.8110 (pttm) REVERT: H 293 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8309 (m) REVERT: H 308 GLU cc_start: 0.7808 (pm20) cc_final: 0.7468 (pm20) REVERT: H 329 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6980 (mt-10) outliers start: 49 outliers final: 27 residues processed: 799 average time/residue: 1.6976 time to fit residues: 1482.8276 Evaluate side-chains 813 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 780 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain D 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 241 MET Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 GLU 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 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 338 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 171 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN C 231 ASN D 72 ASN F 231 ASN H 63 ASN H 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107092 restraints weight = 27805.247| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.91 r_work: 0.3323 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19776 Z= 0.149 Angle : 0.558 7.708 26808 Z= 0.303 Chirality : 0.047 0.159 2936 Planarity : 0.005 0.062 3464 Dihedral : 4.596 16.880 2672 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.67 % Allowed : 22.50 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.17), residues: 2424 helix: -2.31 (0.43), residues: 96 sheet: 0.03 (0.14), residues: 1400 loop : -1.49 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 217 PHE 0.011 0.001 PHE D 100 TYR 0.029 0.001 TYR F 237 ARG 0.007 0.001 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 936) hydrogen bonds : angle 4.79914 ( 3267) covalent geometry : bond 0.00323 (19776) covalent geometry : angle 0.55819 (26808) *********************** 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 822 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 786 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.7606 (m-30) cc_final: 0.7368 (m-30) REVERT: B 75 SER cc_start: 0.8704 (t) cc_final: 0.8382 (p) REVERT: B 202 ASP cc_start: 0.7997 (m-30) cc_final: 0.7657 (m-30) REVERT: B 258 LYS cc_start: 0.8893 (ptpp) cc_final: 0.8597 (ptpp) REVERT: B 308 GLU cc_start: 0.7815 (pm20) cc_final: 0.7460 (pm20) REVERT: A 105 LEU cc_start: 0.8938 (tp) cc_final: 0.8725 (tt) REVERT: A 159 LYS cc_start: 0.8443 (pttm) cc_final: 0.8025 (pttm) REVERT: A 226 ASP cc_start: 0.7778 (t0) cc_final: 0.7327 (t0) REVERT: A 294 SER cc_start: 0.8536 (t) cc_final: 0.8300 (p) REVERT: A 308 GLU cc_start: 0.7744 (pm20) cc_final: 0.7433 (pm20) REVERT: A 321 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7755 (mmmt) REVERT: C 33 VAL cc_start: 0.8706 (p) cc_final: 0.8395 (t) REVERT: C 66 ASP cc_start: 0.8082 (t0) cc_final: 0.7668 (t0) REVERT: C 72 ASN cc_start: 0.8200 (m-40) cc_final: 0.7479 (m-40) REVERT: C 106 ARG cc_start: 0.8324 (mtp85) cc_final: 0.8070 (mtp180) REVERT: C 202 ASP cc_start: 0.7854 (m-30) cc_final: 0.7555 (m-30) REVERT: C 258 LYS cc_start: 0.8856 (ptpp) cc_final: 0.8526 (ptpp) REVERT: C 303 ARG cc_start: 0.8660 (mtt90) cc_final: 0.8394 (mtt180) REVERT: C 308 GLU cc_start: 0.7836 (pm20) cc_final: 0.7400 (pm20) REVERT: C 322 GLU cc_start: 0.8330 (pt0) cc_final: 0.8068 (pt0) REVERT: C 329 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6637 (mt-10) REVERT: C 330 ASP cc_start: 0.7959 (p0) cc_final: 0.7747 (p0) REVERT: D 41 GLU cc_start: 0.7936 (tt0) cc_final: 0.7715 (tt0) REVERT: D 132 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8237 (ttpt) REVERT: D 159 LYS cc_start: 0.8572 (pttm) cc_final: 0.8248 (pttm) REVERT: D 308 GLU cc_start: 0.7751 (pm20) cc_final: 0.7419 (pm20) REVERT: D 321 LYS cc_start: 0.8097 (mtpp) cc_final: 0.7863 (mtpp) REVERT: E 37 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: E 41 GLU cc_start: 0.7935 (tt0) cc_final: 0.7692 (tt0) REVERT: E 62 TYR cc_start: 0.8607 (m-80) cc_final: 0.8069 (m-80) REVERT: E 133 LYS cc_start: 0.8531 (tttm) cc_final: 0.8044 (tttm) REVERT: E 137 GLU cc_start: 0.7749 (mp0) cc_final: 0.7398 (mp0) REVERT: E 202 ASP cc_start: 0.7847 (m-30) cc_final: 0.7485 (m-30) REVERT: E 203 TYR cc_start: 0.8803 (m-80) cc_final: 0.8545 (m-80) REVERT: E 218 ASP cc_start: 0.7709 (m-30) cc_final: 0.7312 (m-30) REVERT: E 237 TYR cc_start: 0.8608 (m-80) cc_final: 0.8282 (m-80) REVERT: E 308 GLU cc_start: 0.7865 (pm20) cc_final: 0.7521 (pm20) REVERT: E 330 ASP cc_start: 0.7915 (p0) cc_final: 0.7690 (p0) REVERT: F 49 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8643 (m) REVERT: F 69 ASP cc_start: 0.7496 (m-30) cc_final: 0.7264 (m-30) REVERT: F 106 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8042 (mtp180) REVERT: F 167 ILE cc_start: 0.8439 (mp) cc_final: 0.8117 (mp) REVERT: F 229 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8135 (m) REVERT: F 308 GLU cc_start: 0.7769 (pm20) cc_final: 0.7415 (pm20) REVERT: F 329 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6975 (mt-10) REVERT: G 33 VAL cc_start: 0.8701 (p) cc_final: 0.8393 (t) REVERT: G 37 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7438 (mt-10) REVERT: G 75 SER cc_start: 0.8647 (t) cc_final: 0.8387 (p) REVERT: G 90 GLU cc_start: 0.7397 (pm20) cc_final: 0.7083 (pm20) REVERT: G 133 LYS cc_start: 0.8578 (tttm) cc_final: 0.8356 (tttp) REVERT: G 258 LYS cc_start: 0.8929 (ptpp) cc_final: 0.8446 (pttm) REVERT: G 308 GLU cc_start: 0.7692 (pm20) cc_final: 0.7238 (pm20) REVERT: G 329 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6927 (mt-10) REVERT: G 340 ARG cc_start: 0.8661 (mmt90) cc_final: 0.8427 (mpt-90) REVERT: H 50 LYS cc_start: 0.8266 (tttp) cc_final: 0.8045 (tttm) REVERT: H 86 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8485 (mmtp) REVERT: H 90 GLU cc_start: 0.7285 (pm20) cc_final: 0.6872 (pm20) REVERT: H 135 ARG cc_start: 0.8359 (tpp80) cc_final: 0.8100 (ttp-170) REVERT: H 159 LYS cc_start: 0.8532 (pttm) cc_final: 0.8145 (pttm) REVERT: H 208 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8471 (pt) REVERT: H 239 ASN cc_start: 0.7993 (t0) cc_final: 0.7751 (t0) REVERT: H 303 ARG cc_start: 0.8480 (mtt90) cc_final: 0.8185 (mtt180) REVERT: H 308 GLU cc_start: 0.7745 (pm20) cc_final: 0.7401 (pm20) REVERT: H 329 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6688 (mt-10) outliers start: 36 outliers final: 22 residues processed: 796 average time/residue: 2.0648 time to fit residues: 1797.6565 Evaluate side-chains 817 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 789 time to evaluate : 2.829 ------------------------------------------------------------------------------- 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 274 MET Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 132 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 F residue 229 THR Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 104 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 77 optimal weight: 0.0870 chunk 181 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN C 56 GLN C 231 ASN F 145 GLN F 231 ASN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.117281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108260 restraints weight = 27829.156| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.93 r_work: 0.3333 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19776 Z= 0.130 Angle : 0.555 7.472 26808 Z= 0.301 Chirality : 0.047 0.155 2936 Planarity : 0.005 0.062 3464 Dihedral : 4.514 23.500 2672 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.30 % Allowed : 22.96 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.17), residues: 2424 helix: -2.23 (0.43), residues: 96 sheet: 0.08 (0.14), residues: 1400 loop : -1.47 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 217 PHE 0.012 0.001 PHE D 100 TYR 0.030 0.001 TYR A 237 ARG 0.008 0.001 ARG G 135 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 936) hydrogen bonds : angle 4.71645 ( 3267) covalent geometry : bond 0.00288 (19776) covalent geometry : angle 0.55455 (26808) ********************** 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 825 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 797 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.7555 (m-30) cc_final: 0.7343 (m-30) REVERT: B 75 SER cc_start: 0.8703 (t) cc_final: 0.8381 (p) REVERT: B 112 LYS cc_start: 0.8124 (mttp) cc_final: 0.7819 (mmmm) REVERT: B 167 ILE cc_start: 0.8509 (tp) cc_final: 0.8236 (tp) REVERT: B 202 ASP cc_start: 0.8001 (m-30) cc_final: 0.7656 (m-30) REVERT: B 258 LYS cc_start: 0.8879 (ptpp) cc_final: 0.8625 (ptpp) REVERT: B 294 SER cc_start: 0.8496 (t) cc_final: 0.8290 (p) REVERT: B 308 GLU cc_start: 0.7817 (pm20) cc_final: 0.7380 (pm20) REVERT: A 105 LEU cc_start: 0.8913 (tp) cc_final: 0.8711 (tt) REVERT: A 226 ASP cc_start: 0.7732 (t0) cc_final: 0.7314 (t0) REVERT: A 294 SER cc_start: 0.8461 (t) cc_final: 0.8258 (p) REVERT: A 308 GLU cc_start: 0.7716 (pm20) cc_final: 0.7413 (pm20) REVERT: C 63 ASN cc_start: 0.8311 (t0) cc_final: 0.8013 (t0) REVERT: C 66 ASP cc_start: 0.8054 (t0) cc_final: 0.7677 (t0) REVERT: C 72 ASN cc_start: 0.8159 (m-40) cc_final: 0.7452 (m-40) REVERT: C 106 ARG cc_start: 0.8320 (mtp85) cc_final: 0.8075 (mtp180) REVERT: C 107 TYR cc_start: 0.8590 (m-80) cc_final: 0.8374 (m-80) REVERT: C 133 LYS cc_start: 0.8625 (ptmm) cc_final: 0.8367 (ptmm) REVERT: C 187 GLU cc_start: 0.7248 (tp30) cc_final: 0.6968 (mp0) REVERT: C 202 ASP cc_start: 0.7816 (m-30) cc_final: 0.7468 (m-30) REVERT: C 226 ASP cc_start: 0.7933 (t70) cc_final: 0.7640 (t70) REVERT: C 258 LYS cc_start: 0.8844 (ptpp) cc_final: 0.8572 (ptpp) REVERT: C 308 GLU cc_start: 0.7817 (pm20) cc_final: 0.7360 (pm20) REVERT: C 322 GLU cc_start: 0.8312 (pt0) cc_final: 0.8066 (pt0) REVERT: C 329 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6569 (mt-10) REVERT: C 330 ASP cc_start: 0.7913 (p0) cc_final: 0.7696 (p0) REVERT: D 41 GLU cc_start: 0.7932 (tt0) cc_final: 0.7710 (tt0) REVERT: D 112 LYS cc_start: 0.7919 (mttp) cc_final: 0.7646 (mttp) REVERT: D 132 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8193 (ttpt) REVERT: D 159 LYS cc_start: 0.8532 (pttm) cc_final: 0.8207 (pttm) REVERT: D 246 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7474 (tpp80) REVERT: D 308 GLU cc_start: 0.7668 (pm20) cc_final: 0.7318 (pm20) REVERT: E 37 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: E 41 GLU cc_start: 0.7917 (tt0) cc_final: 0.7655 (tt0) REVERT: E 62 TYR cc_start: 0.8592 (m-80) cc_final: 0.8026 (m-80) REVERT: E 133 LYS cc_start: 0.8543 (tttm) cc_final: 0.7961 (tttm) REVERT: E 135 ARG cc_start: 0.8426 (tpp80) cc_final: 0.8012 (tpp80) REVERT: E 137 GLU cc_start: 0.7709 (mp0) cc_final: 0.7340 (mp0) REVERT: E 202 ASP cc_start: 0.7859 (m-30) cc_final: 0.7477 (m-30) REVERT: E 218 ASP cc_start: 0.7706 (m-30) cc_final: 0.7185 (m-30) REVERT: E 237 TYR cc_start: 0.8578 (m-80) cc_final: 0.8221 (m-80) REVERT: E 296 MET cc_start: 0.8130 (mpp) cc_final: 0.7627 (mpp) REVERT: E 308 GLU cc_start: 0.7827 (pm20) cc_final: 0.7478 (pm20) REVERT: E 330 ASP cc_start: 0.7940 (p0) cc_final: 0.7735 (p0) REVERT: F 50 LYS cc_start: 0.8203 (tttt) cc_final: 0.7582 (tttm) REVERT: F 69 ASP cc_start: 0.7458 (m-30) cc_final: 0.7216 (m-30) REVERT: F 106 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8049 (mtp180) REVERT: F 229 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8080 (m) REVERT: F 308 GLU cc_start: 0.7756 (pm20) cc_final: 0.7394 (pm20) REVERT: F 329 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6996 (mt-10) REVERT: G 33 VAL cc_start: 0.8690 (p) cc_final: 0.8393 (t) REVERT: G 37 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7434 (mt-10) REVERT: G 75 SER cc_start: 0.8677 (t) cc_final: 0.8416 (p) REVERT: G 90 GLU cc_start: 0.7330 (pm20) cc_final: 0.7014 (pm20) REVERT: G 135 ARG cc_start: 0.8383 (tpp80) cc_final: 0.8176 (tpp80) REVERT: G 258 LYS cc_start: 0.8912 (ptpp) cc_final: 0.8457 (pttm) REVERT: G 301 ILE cc_start: 0.8762 (mp) cc_final: 0.8520 (mt) REVERT: G 329 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6848 (mt-10) REVERT: H 90 GLU cc_start: 0.7278 (pm20) cc_final: 0.6898 (pm20) REVERT: H 135 ARG cc_start: 0.8303 (tpp80) cc_final: 0.7897 (ttp-170) REVERT: H 159 LYS cc_start: 0.8502 (pttm) cc_final: 0.8132 (pttm) REVERT: H 208 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8362 (pt) REVERT: H 308 GLU cc_start: 0.7740 (pm20) cc_final: 0.7417 (pm20) REVERT: H 329 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6526 (mt-10) outliers start: 28 outliers final: 23 residues processed: 803 average time/residue: 2.0876 time to fit residues: 1835.2134 Evaluate side-chains 809 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 781 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 132 LYS 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 229 THR Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 229 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 72 optimal weight: 0.5980 chunk 181 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 231 ASN F 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 = 0.3541 r_free = 0.3541 target = 0.115869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106818 restraints weight = 27993.363| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.94 r_work: 0.3319 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19776 Z= 0.185 Angle : 0.590 11.717 26808 Z= 0.317 Chirality : 0.048 0.158 2936 Planarity : 0.005 0.062 3464 Dihedral : 4.610 22.671 2672 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.53 % Allowed : 23.75 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2424 helix: -2.13 (0.44), residues: 96 sheet: 0.07 (0.14), residues: 1400 loop : -1.48 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 217 PHE 0.009 0.001 PHE B 333 TYR 0.034 0.001 TYR F 237 ARG 0.008 0.001 ARG G 135 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 936) hydrogen bonds : angle 4.74517 ( 3267) covalent geometry : bond 0.00403 (19776) covalent geometry : angle 0.58968 (26808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23888.23 seconds wall clock time: 414 minutes 39.83 seconds (24879.83 seconds total)