Starting phenix.real_space_refine on Thu Feb 5 07:08:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e66_47551/02_2026/9e66_47551.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e66_47551/02_2026/9e66_47551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e66_47551/02_2026/9e66_47551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e66_47551/02_2026/9e66_47551.map" model { file = "/net/cci-nas-00/data/ceres_data/9e66_47551/02_2026/9e66_47551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e66_47551/02_2026/9e66_47551.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 10017 2.51 5 N 2548 2.21 5 O 2723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15344 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2104 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'PHE:plan': 7, 'HIS:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2104 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'PHE:plan': 7, 'HIS:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "C" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2104 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'PHE:plan': 7, 'HIS:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "D" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2104 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'PHE:plan': 7, 'HIS:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "E" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2104 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'PHE:plan': 7, 'HIS:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "F" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2104 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'PHE:plan': 7, 'HIS:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "G" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2104 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'PHE:plan': 7, 'HIS:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 88 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PTY:plan-1': 7, 'PTY:plan-2': 7} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 88 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PTY:plan-1': 7, 'PTY:plan-2': 7} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 88 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PTY:plan-1': 7, 'PTY:plan-2': 7} Unresolved non-hydrogen planarities: 54 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 88 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PTY:plan-1': 7, 'PTY:plan-2': 7} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 88 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PTY:plan-1': 7, 'PTY:plan-2': 7} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 88 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PTY:plan-1': 7, 'PTY:plan-2': 7} Unresolved non-hydrogen planarities: 54 Chain: "G" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 88 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PTY:plan-1': 7, 'PTY:plan-2': 7} Unresolved non-hydrogen planarities: 54 Time building chain proxies: 4.30, per 1000 atoms: 0.28 Number of scatterers: 15344 At special positions: 0 Unit cell: (98.04, 97.18, 135.88, 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 56 16.00 O 2723 8.00 N 2548 7.00 C 10017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 656.5 milliseconds 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3850 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 15 sheets defined 58.2% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 40 through 69 removed outlier: 4.100A pdb=" N LYS A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 111 through 134 removed outlier: 3.855A pdb=" N TYR A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 176 removed outlier: 5.531A pdb=" N ASP A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 265 removed outlier: 4.276A pdb=" N GLY A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'B' and resid 41 through 69 removed outlier: 4.104A pdb=" N LYS B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 4.326A pdb=" N ILE B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 111 through 134 removed outlier: 3.927A pdb=" N TYR B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 176 removed outlier: 5.548A pdb=" N ASP B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 263 removed outlier: 4.262A pdb=" N GLY B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'C' and resid 41 through 69 removed outlier: 4.104A pdb=" N LYS C 69 " --> pdb=" O ILE C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 4.302A pdb=" N ILE C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 111 through 134 removed outlier: 4.023A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 176 removed outlier: 5.549A pdb=" N ASP C 162 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 263 removed outlier: 4.274A pdb=" N GLY C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'D' and resid 41 through 69 removed outlier: 4.096A pdb=" N LYS D 69 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 4.211A pdb=" N ILE D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 111 through 134 removed outlier: 3.898A pdb=" N TYR D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 176 removed outlier: 5.381A pdb=" N ASP D 162 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 247 through 265 removed outlier: 4.268A pdb=" N GLY D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'E' and resid 41 through 69 removed outlier: 4.101A pdb=" N LYS E 69 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 4.403A pdb=" N ILE E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 111 through 134 removed outlier: 3.753A pdb=" N TYR E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 176 removed outlier: 5.548A pdb=" N ASP E 162 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 223 Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 265 removed outlier: 4.270A pdb=" N GLY E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 320 Processing helix chain 'F' and resid 41 through 69 removed outlier: 4.096A pdb=" N LYS F 69 " --> pdb=" O ILE F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 99 removed outlier: 4.384A pdb=" N ILE F 78 " --> pdb=" O THR F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.511A pdb=" N ILE F 106 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 134 removed outlier: 3.728A pdb=" N TYR F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 176 removed outlier: 5.539A pdb=" N ASP F 162 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE F 163 " --> pdb=" O ALA F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 223 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 244 through 246 No H-bonds generated for 'chain 'F' and resid 244 through 246' Processing helix chain 'F' and resid 247 through 263 removed outlier: 4.254A pdb=" N GLY F 252 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 320 Processing helix chain 'G' and resid 41 through 69 removed outlier: 4.103A pdb=" N LYS G 69 " --> pdb=" O ILE G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 99 Processing helix chain 'G' and resid 102 through 106 removed outlier: 3.515A pdb=" N ILE G 106 " --> pdb=" O LYS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 134 removed outlier: 3.855A pdb=" N TYR G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 176 removed outlier: 5.515A pdb=" N ASP G 162 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 244 through 246 No H-bonds generated for 'chain 'G' and resid 244 through 246' Processing helix chain 'G' and resid 247 through 263 removed outlier: 4.265A pdb=" N GLY G 252 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.684A pdb=" N LYS A 205 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE A 199 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 7.285A pdb=" N ILE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE B 199 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS B 205 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 243 removed outlier: 3.995A pdb=" N ARG A 235 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN A 287 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 333 removed outlier: 6.748A pdb=" N GLN A 329 " --> pdb=" O TYR G 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 226 through 227 removed outlier: 7.145A pdb=" N ILE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE C 199 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS C 205 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 235 through 243 removed outlier: 3.981A pdb=" N ARG B 235 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN B 287 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 226 through 227 removed outlier: 7.264A pdb=" N ILE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE D 199 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS D 205 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 243 removed outlier: 3.993A pdb=" N ARG C 235 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN C 280 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET C 289 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE C 278 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TYR C 291 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL C 276 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 226 through 227 removed outlier: 7.286A pdb=" N ILE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE E 199 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS E 205 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 235 through 243 removed outlier: 4.013A pdb=" N ARG D 235 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN D 287 " --> pdb=" O ASN D 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 226 through 227 removed outlier: 7.274A pdb=" N ILE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE F 199 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS F 205 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 235 through 243 removed outlier: 4.022A pdb=" N ARG E 235 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN E 287 " --> pdb=" O ASN E 279 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 226 through 227 removed outlier: 7.275A pdb=" N ILE G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ILE G 199 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS G 205 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 235 through 243 removed outlier: 4.039A pdb=" N ARG F 235 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN F 287 " --> pdb=" O ASN F 279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 235 through 243 removed outlier: 4.032A pdb=" N ARG G 235 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN G 287 " --> pdb=" O ASN G 279 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 3090 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 1.76 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: 4921 1.34 - 1.46: 2918 1.46 - 1.58: 7617 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 15561 Sorted by residual: bond pdb=" CB GLU A 136 " pdb=" CG GLU A 136 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" CB GLU E 136 " pdb=" CG GLU E 136 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.82e+00 bond pdb=" CB GLU G 136 " pdb=" CG GLU G 136 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CB GLU F 136 " pdb=" CG GLU F 136 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CA GLU G 136 " pdb=" CB GLU G 136 " ideal model delta sigma weight residual 1.528 1.547 -0.018 1.66e-02 3.63e+03 1.20e+00 ... (remaining 15556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 20654 2.27 - 4.54: 229 4.54 - 6.81: 41 6.81 - 9.08: 25 9.08 - 11.35: 23 Bond angle restraints: 20972 Sorted by residual: angle pdb=" CA ILE E 151 " pdb=" CB ILE E 151 " pdb=" CG1 ILE E 151 " ideal model delta sigma weight residual 110.40 116.40 -6.00 1.70e+00 3.46e-01 1.25e+01 angle pdb=" CA GLU G 136 " pdb=" CB GLU G 136 " pdb=" CG GLU G 136 " ideal model delta sigma weight residual 114.10 121.16 -7.06 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CA GLU A 136 " pdb=" CB GLU A 136 " pdb=" CG GLU A 136 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA ILE A 151 " pdb=" CB ILE A 151 " pdb=" CG1 ILE A 151 " ideal model delta sigma weight residual 110.40 116.32 -5.92 1.70e+00 3.46e-01 1.21e+01 angle pdb=" CA ILE C 151 " pdb=" CB ILE C 151 " pdb=" CG1 ILE C 151 " ideal model delta sigma weight residual 110.40 116.31 -5.91 1.70e+00 3.46e-01 1.21e+01 ... (remaining 20967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 8258 15.68 - 31.35: 708 31.35 - 47.03: 184 47.03 - 62.70: 111 62.70 - 78.38: 7 Dihedral angle restraints: 9268 sinusoidal: 3304 harmonic: 5964 Sorted by residual: dihedral pdb=" CA GLY D 139 " pdb=" C GLY D 139 " pdb=" N MET D 140 " pdb=" CA MET D 140 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CG ARG C 271 " pdb=" CD ARG C 271 " pdb=" NE ARG C 271 " pdb=" CZ ARG C 271 " ideal model delta sinusoidal sigma weight residual -90.00 -42.32 -47.68 2 1.50e+01 4.44e-03 1.17e+01 dihedral pdb=" CA GLN D 318 " pdb=" CB GLN D 318 " pdb=" CG GLN D 318 " pdb=" CD GLN D 318 " ideal model delta sinusoidal sigma weight residual -60.00 -119.88 59.88 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 9265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1604 0.040 - 0.080: 651 0.080 - 0.119: 152 0.119 - 0.159: 31 0.159 - 0.199: 5 Chirality restraints: 2443 Sorted by residual: chirality pdb=" CB ILE E 127 " pdb=" CA ILE E 127 " pdb=" CG1 ILE E 127 " pdb=" CG2 ILE E 127 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CB ILE G 127 " pdb=" CA ILE G 127 " pdb=" CG1 ILE G 127 " pdb=" CG2 ILE G 127 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CB ILE F 127 " pdb=" CA ILE F 127 " pdb=" CG1 ILE F 127 " pdb=" CG2 ILE F 127 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.57e-01 ... (remaining 2440 not shown) Planarity restraints: 2639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU F 136 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.33e+00 pdb=" CD GLU F 136 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU F 136 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU F 136 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 271 " 0.130 9.50e-02 1.11e+02 5.86e-02 2.76e+00 pdb=" NE ARG E 271 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 271 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E 271 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG E 271 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 271 " 0.129 9.50e-02 1.11e+02 5.81e-02 2.74e+00 pdb=" NE ARG G 271 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG G 271 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG G 271 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 271 " -0.000 2.00e-02 2.50e+03 ... (remaining 2636 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 545 2.72 - 3.26: 14841 3.26 - 3.81: 24648 3.81 - 4.35: 27971 4.35 - 4.90: 49513 Nonbonded interactions: 117518 Sorted by model distance: nonbonded pdb=" N GLU B 246 " pdb=" OE1 GLU B 246 " model vdw 2.172 3.120 nonbonded pdb=" N GLU G 246 " pdb=" OE1 GLU G 246 " model vdw 2.219 3.120 nonbonded pdb=" N GLU F 246 " pdb=" OE1 GLU F 246 " model vdw 2.220 3.120 nonbonded pdb=" N GLU D 246 " pdb=" OE1 GLU D 246 " model vdw 2.234 3.120 nonbonded pdb=" N GLU A 246 " pdb=" OE1 GLU A 246 " model vdw 2.240 3.120 ... (remaining 117513 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 334 or (resid 401 and (name C20 or name C21 or \ name C22 or name C23 or name C24 or name C25)) or (resid 402 and (name C18 or na \ me C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29)) or resid 403 or (resid 404 and \ (name C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C2 \ 5 or name C26 or name C27 or name C28 or name C29)) or (resid 405 through 406 an \ d (name C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25)) or (resid 407 and (name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C29)))) selection = (chain 'B' and (resid 40 through 334 or (resid 401 and (name C20 or name C21 or \ name C22 or name C23 or name C24 or name C25)) or resid 402 or (resid 403 and (n \ ame C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29)) or resid 404 or (resid 405 through 406 and \ (name C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C \ 25)) or resid 407)) selection = (chain 'C' and (resid 40 through 334 or (resid 401 and (name C20 or name C21 or \ name C22 or name C23 or name C24 or name C25)) or resid 402 or (resid 403 and (n \ ame C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29)) or resid 404 or (resid 405 through 406 and \ (name C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C \ 25)) or resid 407)) selection = (chain 'D' and (resid 40 through 334 or (resid 401 and (name C20 or name C21 or \ name C22 or name C23 or name C24 or name C25)) or resid 402 or (resid 403 and (n \ ame C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29)) or resid 404 or (resid 405 through 406 and \ (name C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C \ 25)) or resid 407)) selection = (chain 'E' and (resid 40 through 334 or (resid 401 and (name C20 or name C21 or \ name C22 or name C23 or name C24 or name C25)) or resid 402 or (resid 403 and (n \ ame C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29)) or resid 404 or (resid 405 through 406 and \ (name C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C \ 25)) or resid 407)) selection = (chain 'F' and (resid 40 through 334 or (resid 401 and (name C20 or name C21 or \ name C22 or name C23 or name C24 or name C25)) or resid 402 or (resid 403 and (n \ ame C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29)) or resid 404 or (resid 405 through 406 and \ (name C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C \ 25)) or resid 407)) selection = (chain 'G' and (resid 40 through 334 or (resid 401 and (name C20 or name C21 or \ name C22 or name C23 or name C24 or name C25)) or (resid 402 and (name C18 or na \ me C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29)) or (resid 403 and (name C20 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29)) or resid 404 or (resid 405 through 406 and (name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25)) or (re \ sid 407 and (name C20 or name C21 or name C22 or name C23 or name C24 or name C2 \ 5 or name C26 or name C27 or name C28 or name C29)))) } 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.350 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15561 Z= 0.131 Angle : 0.716 11.347 20972 Z= 0.340 Chirality : 0.045 0.199 2443 Planarity : 0.004 0.059 2639 Dihedral : 14.568 78.381 5418 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.68 % Allowed : 3.66 % Favored : 95.66 % Rotamer: Outliers : 1.45 % Allowed : 26.36 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.18), residues: 2051 helix: 3.01 (0.15), residues: 1036 sheet: 0.32 (0.32), residues: 259 loop : -1.57 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 271 TYR 0.010 0.001 TYR C 291 PHE 0.023 0.001 PHE B 148 TRP 0.006 0.001 TRP B 201 HIS 0.002 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00278 (15561) covalent geometry : angle 0.71647 (20972) hydrogen bonds : bond 0.12393 ( 1090) hydrogen bonds : angle 5.06600 ( 3090) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 0.549 Fit side-chains REVERT: A 176 ASP cc_start: 0.7498 (t0) cc_final: 0.7185 (t0) REVERT: A 191 ASN cc_start: 0.9392 (t0) cc_final: 0.9163 (t0) REVERT: B 137 HIS cc_start: 0.8704 (m90) cc_final: 0.8382 (m90) REVERT: B 323 ASP cc_start: 0.9366 (t0) cc_final: 0.9127 (t0) REVERT: F 134 TYR cc_start: 0.7638 (m-80) cc_final: 0.6935 (t80) REVERT: F 136 GLU cc_start: 0.9224 (pp20) cc_final: 0.8797 (pp20) REVERT: G 146 LEU cc_start: 0.8981 (tt) cc_final: 0.8641 (tp) REVERT: G 176 ASP cc_start: 0.7368 (t0) cc_final: 0.7150 (t0) REVERT: G 323 ASP cc_start: 0.9338 (t0) cc_final: 0.9074 (t0) outliers start: 19 outliers final: 15 residues processed: 258 average time/residue: 0.6200 time to fit residues: 174.8491 Evaluate side-chains 253 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 319 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS D 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.096768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.060001 restraints weight = 36913.875| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.00 r_work: 0.2569 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15561 Z= 0.118 Angle : 0.614 9.915 20972 Z= 0.295 Chirality : 0.043 0.137 2443 Planarity : 0.003 0.028 2639 Dihedral : 5.659 46.205 2685 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.61 % Favored : 95.81 % Rotamer: Outliers : 1.45 % Allowed : 21.85 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.19), residues: 2051 helix: 3.33 (0.15), residues: 1050 sheet: -0.12 (0.33), residues: 273 loop : -1.40 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 271 TYR 0.013 0.001 TYR A 291 PHE 0.013 0.001 PHE D 138 TRP 0.004 0.001 TRP A 201 HIS 0.004 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00249 (15561) covalent geometry : angle 0.61362 (20972) hydrogen bonds : bond 0.03498 ( 1090) hydrogen bonds : angle 3.52099 ( 3090) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 253 time to evaluate : 0.482 Fit side-chains REVERT: A 134 TYR cc_start: 0.8148 (m-80) cc_final: 0.7914 (m-80) REVERT: A 136 GLU cc_start: 0.9091 (pp20) cc_final: 0.8727 (pp20) REVERT: A 137 HIS cc_start: 0.8858 (OUTLIER) cc_final: 0.8451 (m90) REVERT: A 176 ASP cc_start: 0.7684 (t0) cc_final: 0.7302 (t0) REVERT: A 191 ASN cc_start: 0.9396 (t0) cc_final: 0.9171 (t0) REVERT: A 280 GLN cc_start: 0.9213 (tt0) cc_final: 0.8571 (tm-30) REVERT: B 137 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.8543 (m90) REVERT: B 260 GLU cc_start: 0.9375 (tp30) cc_final: 0.8820 (tp30) REVERT: B 280 GLN cc_start: 0.9248 (tt0) cc_final: 0.8607 (tm-30) REVERT: C 176 ASP cc_start: 0.7565 (t0) cc_final: 0.7285 (t0) REVERT: C 260 GLU cc_start: 0.9354 (tp30) cc_final: 0.8827 (tp30) REVERT: D 176 ASP cc_start: 0.7600 (t0) cc_final: 0.7207 (t0) REVERT: E 176 ASP cc_start: 0.7784 (t0) cc_final: 0.7434 (t0) REVERT: E 250 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8823 (mtpp) REVERT: E 260 GLU cc_start: 0.9223 (tp30) cc_final: 0.8862 (mm-30) REVERT: F 172 MET cc_start: 0.8743 (tmm) cc_final: 0.8441 (tmm) REVERT: F 260 GLU cc_start: 0.9326 (tp30) cc_final: 0.8723 (tp30) REVERT: F 280 GLN cc_start: 0.9209 (tt0) cc_final: 0.8492 (tm-30) REVERT: F 308 ASP cc_start: 0.9286 (t0) cc_final: 0.8955 (t0) REVERT: G 146 LEU cc_start: 0.8885 (tt) cc_final: 0.8518 (tp) REVERT: G 172 MET cc_start: 0.8748 (tmm) cc_final: 0.8482 (tmm) REVERT: G 176 ASP cc_start: 0.7639 (t0) cc_final: 0.7118 (t0) REVERT: G 260 GLU cc_start: 0.9369 (tp30) cc_final: 0.8815 (tp30) REVERT: G 289 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.9154 (ppp) outliers start: 19 outliers final: 4 residues processed: 257 average time/residue: 0.6849 time to fit residues: 191.5996 Evaluate side-chains 254 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 246 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 289 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 145 optimal weight: 70.0000 chunk 20 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 6 optimal weight: 50.0000 chunk 199 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 50.0000 chunk 92 optimal weight: 5.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS E 137 HIS F 137 HIS G 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.093551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.056787 restraints weight = 37903.459| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.99 r_work: 0.2496 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15561 Z= 0.228 Angle : 0.638 9.785 20972 Z= 0.315 Chirality : 0.046 0.135 2443 Planarity : 0.003 0.031 2639 Dihedral : 6.215 53.533 2667 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.73 % Favored : 94.93 % Rotamer: Outliers : 2.60 % Allowed : 21.01 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.19), residues: 2051 helix: 2.79 (0.15), residues: 1141 sheet: 0.16 (0.35), residues: 245 loop : -1.36 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 271 TYR 0.016 0.001 TYR A 291 PHE 0.014 0.001 PHE A 148 TRP 0.009 0.001 TRP B 184 HIS 0.010 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00531 (15561) covalent geometry : angle 0.63775 (20972) hydrogen bonds : bond 0.04543 ( 1090) hydrogen bonds : angle 3.60672 ( 3090) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 0.589 Fit side-chains REVERT: A 136 GLU cc_start: 0.8986 (pp20) cc_final: 0.8750 (pp20) REVERT: A 137 HIS cc_start: 0.8899 (OUTLIER) cc_final: 0.8488 (m90) REVERT: A 176 ASP cc_start: 0.7775 (t0) cc_final: 0.7548 (t0) REVERT: A 250 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.8892 (mmtm) REVERT: A 260 GLU cc_start: 0.9265 (tp30) cc_final: 0.8891 (mm-30) REVERT: A 315 ASP cc_start: 0.9459 (t0) cc_final: 0.9252 (t0) REVERT: B 137 HIS cc_start: 0.8878 (OUTLIER) cc_final: 0.8524 (m90) REVERT: B 250 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8733 (mtpp) REVERT: B 260 GLU cc_start: 0.9399 (tp30) cc_final: 0.8833 (tp30) REVERT: C 137 HIS cc_start: 0.8901 (OUTLIER) cc_final: 0.8683 (m90) REVERT: C 260 GLU cc_start: 0.9364 (tp30) cc_final: 0.8833 (tp30) REVERT: D 176 ASP cc_start: 0.7812 (t0) cc_final: 0.7588 (t0) REVERT: D 260 GLU cc_start: 0.9255 (tp30) cc_final: 0.8598 (tp30) REVERT: E 176 ASP cc_start: 0.7984 (t0) cc_final: 0.7751 (t0) REVERT: E 250 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8890 (mttp) REVERT: E 260 GLU cc_start: 0.9251 (tp30) cc_final: 0.8565 (tp30) REVERT: E 308 ASP cc_start: 0.9428 (t0) cc_final: 0.9184 (t0) REVERT: E 315 ASP cc_start: 0.9530 (t0) cc_final: 0.9274 (t0) REVERT: F 146 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8527 (tm) REVERT: F 172 MET cc_start: 0.8889 (tmm) cc_final: 0.8479 (tmm) REVERT: F 250 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8755 (mtpp) REVERT: F 260 GLU cc_start: 0.9364 (tp30) cc_final: 0.8784 (tp30) REVERT: F 308 ASP cc_start: 0.9344 (t0) cc_final: 0.9011 (t0) REVERT: G 146 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8579 (tp) REVERT: G 176 ASP cc_start: 0.7959 (t0) cc_final: 0.7626 (t0) REVERT: G 260 GLU cc_start: 0.9387 (tp30) cc_final: 0.8853 (tp30) outliers start: 34 outliers final: 10 residues processed: 266 average time/residue: 0.5906 time to fit residues: 171.9378 Evaluate side-chains 263 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 289 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 109 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 149 optimal weight: 40.0000 chunk 165 optimal weight: 4.9990 chunk 162 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 50.0000 chunk 190 optimal weight: 4.9990 chunk 62 optimal weight: 40.0000 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS E 137 HIS F 137 HIS G 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.095757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.059343 restraints weight = 36941.126| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 2.98 r_work: 0.2537 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15561 Z= 0.124 Angle : 0.627 10.658 20972 Z= 0.298 Chirality : 0.044 0.158 2443 Planarity : 0.003 0.033 2639 Dihedral : 5.932 53.056 2667 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.00 % Favored : 95.66 % Rotamer: Outliers : 2.06 % Allowed : 22.84 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.19), residues: 2051 helix: 3.46 (0.15), residues: 1057 sheet: -0.19 (0.34), residues: 273 loop : -1.50 (0.20), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 271 TYR 0.013 0.001 TYR A 291 PHE 0.017 0.001 PHE B 148 TRP 0.005 0.001 TRP A 201 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00274 (15561) covalent geometry : angle 0.62733 (20972) hydrogen bonds : bond 0.03469 ( 1090) hydrogen bonds : angle 3.33121 ( 3090) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 263 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 176 ASP cc_start: 0.7705 (t0) cc_final: 0.7445 (t0) REVERT: A 250 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8785 (mmtm) REVERT: A 260 GLU cc_start: 0.9276 (tp30) cc_final: 0.8529 (tp30) REVERT: A 315 ASP cc_start: 0.9479 (t0) cc_final: 0.9240 (t0) REVERT: B 137 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.8538 (m90) REVERT: B 176 ASP cc_start: 0.7666 (t0) cc_final: 0.7449 (t0) REVERT: B 250 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8809 (mtpp) REVERT: B 260 GLU cc_start: 0.9409 (tp30) cc_final: 0.8808 (tp30) REVERT: C 137 HIS cc_start: 0.8831 (OUTLIER) cc_final: 0.8620 (m90) REVERT: C 140 MET cc_start: 0.7891 (mpm) cc_final: 0.7575 (mpm) REVERT: C 172 MET cc_start: 0.8825 (tmm) cc_final: 0.8529 (tmm) REVERT: C 260 GLU cc_start: 0.9370 (tp30) cc_final: 0.8848 (tp30) REVERT: D 176 ASP cc_start: 0.7705 (t0) cc_final: 0.7451 (t0) REVERT: D 260 GLU cc_start: 0.9250 (tp30) cc_final: 0.8604 (tp30) REVERT: E 176 ASP cc_start: 0.7826 (t0) cc_final: 0.7522 (t0) REVERT: E 250 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8721 (mttp) REVERT: E 260 GLU cc_start: 0.9247 (tp30) cc_final: 0.8588 (tp30) REVERT: F 146 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8495 (tm) REVERT: F 172 MET cc_start: 0.8819 (tmm) cc_final: 0.8407 (tmm) REVERT: F 176 ASP cc_start: 0.7698 (t0) cc_final: 0.6975 (t0) REVERT: F 250 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8714 (mtpp) REVERT: F 260 GLU cc_start: 0.9379 (tp30) cc_final: 0.8766 (tp30) REVERT: G 146 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8562 (tp) REVERT: G 172 MET cc_start: 0.8827 (tmm) cc_final: 0.8564 (tmm) REVERT: G 176 ASP cc_start: 0.7751 (t0) cc_final: 0.7322 (t0) REVERT: G 260 GLU cc_start: 0.9381 (tp30) cc_final: 0.8823 (tp30) outliers start: 27 outliers final: 10 residues processed: 267 average time/residue: 0.6268 time to fit residues: 183.0015 Evaluate side-chains 270 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 252 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 289 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 121 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 40.0000 chunk 127 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 0 optimal weight: 70.0000 chunk 165 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS E 137 HIS F 137 HIS G 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.095228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.058794 restraints weight = 37162.648| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.99 r_work: 0.2537 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15561 Z= 0.143 Angle : 0.630 10.487 20972 Z= 0.301 Chirality : 0.044 0.152 2443 Planarity : 0.003 0.039 2639 Dihedral : 5.929 56.150 2667 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.19 % Favored : 95.47 % Rotamer: Outliers : 2.75 % Allowed : 23.30 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.19), residues: 2051 helix: 3.52 (0.15), residues: 1057 sheet: -0.20 (0.34), residues: 273 loop : -1.50 (0.20), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 271 TYR 0.023 0.001 TYR C 134 PHE 0.019 0.001 PHE A 148 TRP 0.006 0.001 TRP G 184 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00326 (15561) covalent geometry : angle 0.63010 (20972) hydrogen bonds : bond 0.03526 ( 1090) hydrogen bonds : angle 3.32865 ( 3090) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 0.415 Fit side-chains REVERT: A 250 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8755 (mmtm) REVERT: A 260 GLU cc_start: 0.9281 (tp30) cc_final: 0.8533 (tp30) REVERT: A 280 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.8931 (tt0) REVERT: A 315 ASP cc_start: 0.9492 (t0) cc_final: 0.9252 (t0) REVERT: B 137 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.8466 (m90) REVERT: B 145 LEU cc_start: 0.8792 (mt) cc_final: 0.8497 (pp) REVERT: B 250 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8845 (mtpp) REVERT: B 260 GLU cc_start: 0.9414 (tp30) cc_final: 0.8844 (tp30) REVERT: C 137 HIS cc_start: 0.8881 (OUTLIER) cc_final: 0.8628 (m90) REVERT: C 140 MET cc_start: 0.7869 (mpm) cc_final: 0.7576 (mpm) REVERT: C 172 MET cc_start: 0.8841 (tmm) cc_final: 0.8569 (tmm) REVERT: C 260 GLU cc_start: 0.9378 (tp30) cc_final: 0.8840 (tp30) REVERT: C 280 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8589 (tm-30) REVERT: D 136 GLU cc_start: 0.9231 (pp20) cc_final: 0.8927 (pp20) REVERT: D 137 HIS cc_start: 0.8849 (OUTLIER) cc_final: 0.8494 (m90) REVERT: D 260 GLU cc_start: 0.9283 (tp30) cc_final: 0.8656 (tp30) REVERT: E 176 ASP cc_start: 0.7836 (t0) cc_final: 0.7614 (t0) REVERT: E 250 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8750 (mttp) REVERT: E 260 GLU cc_start: 0.9250 (tp30) cc_final: 0.8593 (tp30) REVERT: E 301 GLU cc_start: 0.9129 (mp0) cc_final: 0.8742 (pm20) REVERT: F 172 MET cc_start: 0.8871 (tmm) cc_final: 0.8453 (tmm) REVERT: F 250 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8718 (mtpp) REVERT: F 260 GLU cc_start: 0.9377 (tp30) cc_final: 0.8767 (tp30) REVERT: F 308 ASP cc_start: 0.9336 (t0) cc_final: 0.9029 (t0) REVERT: G 146 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8688 (tm) REVERT: G 176 ASP cc_start: 0.7854 (t0) cc_final: 0.7501 (t0) REVERT: G 260 GLU cc_start: 0.9368 (tp30) cc_final: 0.8807 (tp30) outliers start: 36 outliers final: 12 residues processed: 271 average time/residue: 0.5886 time to fit residues: 174.3008 Evaluate side-chains 279 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 257 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 289 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 74 optimal weight: 4.9990 chunk 149 optimal weight: 40.0000 chunk 122 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 134 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 137 HIS F 137 HIS G 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.095798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.059366 restraints weight = 36910.771| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.99 r_work: 0.2551 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15561 Z= 0.120 Angle : 0.643 10.745 20972 Z= 0.303 Chirality : 0.044 0.160 2443 Planarity : 0.003 0.044 2639 Dihedral : 5.838 58.396 2667 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.90 % Favored : 95.76 % Rotamer: Outliers : 2.22 % Allowed : 23.83 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.19), residues: 2051 helix: 3.61 (0.15), residues: 1050 sheet: -0.22 (0.33), residues: 273 loop : -1.57 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 271 TYR 0.013 0.001 TYR A 291 PHE 0.018 0.001 PHE F 148 TRP 0.005 0.001 TRP G 184 HIS 0.002 0.001 HIS F 320 Details of bonding type rmsd covalent geometry : bond 0.00267 (15561) covalent geometry : angle 0.64264 (20972) hydrogen bonds : bond 0.03218 ( 1090) hydrogen bonds : angle 3.24702 ( 3090) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 0.507 Fit side-chains REVERT: A 250 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8738 (mmtm) REVERT: A 260 GLU cc_start: 0.9274 (tp30) cc_final: 0.8540 (tp30) REVERT: A 280 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.8658 (tm-30) REVERT: A 315 ASP cc_start: 0.9500 (t0) cc_final: 0.9262 (t0) REVERT: B 137 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.8433 (m90) REVERT: B 145 LEU cc_start: 0.8793 (mt) cc_final: 0.8489 (pp) REVERT: B 176 ASP cc_start: 0.7752 (t0) cc_final: 0.7545 (t0) REVERT: B 260 GLU cc_start: 0.9417 (tp30) cc_final: 0.8830 (tp30) REVERT: C 137 HIS cc_start: 0.8837 (OUTLIER) cc_final: 0.8537 (m-70) REVERT: C 140 MET cc_start: 0.7799 (mpm) cc_final: 0.7547 (mpm) REVERT: C 172 MET cc_start: 0.8836 (tmm) cc_final: 0.8533 (tmm) REVERT: C 260 GLU cc_start: 0.9393 (tp30) cc_final: 0.8869 (tp30) REVERT: C 280 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8586 (tm-30) REVERT: D 137 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.8469 (m90) REVERT: D 260 GLU cc_start: 0.9311 (tp30) cc_final: 0.8679 (tp30) REVERT: E 250 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8719 (mttp) REVERT: E 260 GLU cc_start: 0.9243 (tp30) cc_final: 0.8572 (tp30) REVERT: E 301 GLU cc_start: 0.9145 (mp0) cc_final: 0.8768 (pm20) REVERT: F 172 MET cc_start: 0.8884 (tmm) cc_final: 0.8446 (tmm) REVERT: F 176 ASP cc_start: 0.7689 (t0) cc_final: 0.6949 (t0) REVERT: F 250 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8720 (mtpp) REVERT: F 260 GLU cc_start: 0.9374 (tp30) cc_final: 0.8748 (tp30) REVERT: G 146 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8690 (tm) REVERT: G 176 ASP cc_start: 0.7728 (t0) cc_final: 0.7467 (t0) REVERT: G 260 GLU cc_start: 0.9374 (tp30) cc_final: 0.8808 (tp30) REVERT: G 289 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.9208 (ppp) outliers start: 29 outliers final: 8 residues processed: 272 average time/residue: 0.5797 time to fit residues: 172.6051 Evaluate side-chains 271 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 253 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 289 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 178 optimal weight: 40.0000 chunk 127 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 chunk 0 optimal weight: 70.0000 chunk 9 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 47 optimal weight: 0.0770 chunk 83 optimal weight: 4.9990 chunk 89 optimal weight: 70.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 137 HIS F 137 HIS G 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.093530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.056903 restraints weight = 37151.613| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.95 r_work: 0.2490 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 15561 Z= 0.270 Angle : 0.705 10.623 20972 Z= 0.345 Chirality : 0.047 0.182 2443 Planarity : 0.004 0.051 2639 Dihedral : 6.372 59.651 2667 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.07 % Favored : 94.59 % Rotamer: Outliers : 2.98 % Allowed : 22.92 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.19), residues: 2051 helix: 3.28 (0.15), residues: 1092 sheet: 0.05 (0.35), residues: 245 loop : -1.79 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 271 TYR 0.018 0.001 TYR A 291 PHE 0.021 0.002 PHE A 148 TRP 0.011 0.002 TRP E 184 HIS 0.004 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00632 (15561) covalent geometry : angle 0.70457 (20972) hydrogen bonds : bond 0.04477 ( 1090) hydrogen bonds : angle 3.57466 ( 3090) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.443 Fit side-chains REVERT: A 137 HIS cc_start: 0.8837 (OUTLIER) cc_final: 0.8533 (m-70) REVERT: A 250 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8835 (mmtm) REVERT: A 260 GLU cc_start: 0.9303 (tp30) cc_final: 0.8823 (tm-30) REVERT: A 315 ASP cc_start: 0.9522 (t0) cc_final: 0.9288 (t0) REVERT: B 137 HIS cc_start: 0.8723 (OUTLIER) cc_final: 0.8510 (m90) REVERT: B 140 MET cc_start: 0.7488 (mmp) cc_final: 0.7265 (mmp) REVERT: B 145 LEU cc_start: 0.8808 (mt) cc_final: 0.8544 (pp) REVERT: B 260 GLU cc_start: 0.9430 (tp30) cc_final: 0.8831 (tp30) REVERT: C 137 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.8645 (m90) REVERT: C 140 MET cc_start: 0.7918 (mpm) cc_final: 0.7669 (mpm) REVERT: C 260 GLU cc_start: 0.9399 (tp30) cc_final: 0.8871 (tp30) REVERT: C 280 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.8559 (tm-30) REVERT: D 136 GLU cc_start: 0.9177 (pp20) cc_final: 0.8915 (pp20) REVERT: D 137 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8456 (m90) REVERT: D 260 GLU cc_start: 0.9332 (tp30) cc_final: 0.8950 (tp30) REVERT: D 264 ASN cc_start: 0.9469 (m-40) cc_final: 0.9116 (m-40) REVERT: E 134 TYR cc_start: 0.8085 (m-80) cc_final: 0.7571 (t80) REVERT: E 137 HIS cc_start: 0.9141 (OUTLIER) cc_final: 0.8913 (m170) REVERT: E 250 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8894 (mttp) REVERT: E 260 GLU cc_start: 0.9250 (tp30) cc_final: 0.8607 (tp30) REVERT: E 301 GLU cc_start: 0.9216 (mp0) cc_final: 0.8845 (pm20) REVERT: F 172 MET cc_start: 0.8949 (tmm) cc_final: 0.8531 (tmm) REVERT: F 250 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8764 (mtpp) REVERT: F 260 GLU cc_start: 0.9380 (tp30) cc_final: 0.8746 (tp30) REVERT: G 260 GLU cc_start: 0.9370 (tp30) cc_final: 0.8800 (tp30) outliers start: 39 outliers final: 14 residues processed: 263 average time/residue: 0.5931 time to fit residues: 170.5206 Evaluate side-chains 264 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain G residue 289 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 53 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 181 optimal weight: 30.0000 chunk 196 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 116 optimal weight: 70.0000 chunk 171 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 137 HIS F 137 HIS G 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.097055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.060597 restraints weight = 37237.104| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.96 r_work: 0.2557 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15561 Z= 0.116 Angle : 0.694 12.554 20972 Z= 0.325 Chirality : 0.045 0.185 2443 Planarity : 0.004 0.051 2639 Dihedral : 5.946 59.779 2667 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.95 % Favored : 95.71 % Rotamer: Outliers : 1.91 % Allowed : 25.52 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.19), residues: 2051 helix: 3.55 (0.15), residues: 1057 sheet: 0.11 (0.34), residues: 259 loop : -1.55 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 271 TYR 0.024 0.001 TYR A 134 PHE 0.021 0.001 PHE C 148 TRP 0.006 0.001 TRP E 302 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00259 (15561) covalent geometry : angle 0.69351 (20972) hydrogen bonds : bond 0.03092 ( 1090) hydrogen bonds : angle 3.26068 ( 3090) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 256 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8709 (mmtm) REVERT: A 260 GLU cc_start: 0.9268 (tp30) cc_final: 0.8849 (tp30) REVERT: A 280 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.8688 (tm-30) REVERT: A 315 ASP cc_start: 0.9521 (t0) cc_final: 0.9256 (t0) REVERT: B 137 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.8460 (m90) REVERT: B 145 LEU cc_start: 0.8812 (mt) cc_final: 0.8436 (pp) REVERT: B 176 ASP cc_start: 0.7792 (t0) cc_final: 0.7572 (t0) REVERT: B 260 GLU cc_start: 0.9421 (tp30) cc_final: 0.8840 (tp30) REVERT: C 137 HIS cc_start: 0.8796 (OUTLIER) cc_final: 0.8541 (m90) REVERT: C 140 MET cc_start: 0.7750 (mpm) cc_final: 0.7495 (mpm) REVERT: C 260 GLU cc_start: 0.9400 (tp30) cc_final: 0.8896 (tp30) REVERT: C 280 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8591 (tm-30) REVERT: D 136 GLU cc_start: 0.9068 (pp20) cc_final: 0.8853 (pp20) REVERT: D 137 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.8331 (m90) REVERT: D 260 GLU cc_start: 0.9313 (tp30) cc_final: 0.9011 (tp30) REVERT: E 250 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8723 (mttp) REVERT: E 260 GLU cc_start: 0.9235 (tp30) cc_final: 0.8587 (tp30) REVERT: E 301 GLU cc_start: 0.9165 (mp0) cc_final: 0.8811 (pm20) REVERT: F 172 MET cc_start: 0.8902 (tmm) cc_final: 0.8431 (tmm) REVERT: F 176 ASP cc_start: 0.7694 (t0) cc_final: 0.6923 (t0) REVERT: F 260 GLU cc_start: 0.9385 (tp30) cc_final: 0.8773 (tp30) REVERT: G 137 HIS cc_start: 0.9052 (OUTLIER) cc_final: 0.8681 (m170) REVERT: G 247 ASP cc_start: 0.9213 (m-30) cc_final: 0.8675 (m-30) REVERT: G 260 GLU cc_start: 0.9383 (tp30) cc_final: 0.8811 (tp30) outliers start: 25 outliers final: 9 residues processed: 263 average time/residue: 0.5960 time to fit residues: 171.1560 Evaluate side-chains 267 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain G residue 137 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 121 optimal weight: 50.0000 chunk 119 optimal weight: 50.0000 chunk 124 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 147 optimal weight: 70.0000 chunk 92 optimal weight: 50.0000 chunk 43 optimal weight: 0.1980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.059049 restraints weight = 36974.849| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.99 r_work: 0.2541 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15561 Z= 0.147 Angle : 0.706 11.145 20972 Z= 0.334 Chirality : 0.045 0.238 2443 Planarity : 0.004 0.058 2639 Dihedral : 5.922 59.756 2667 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.44 % Favored : 95.22 % Rotamer: Outliers : 1.07 % Allowed : 26.13 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.19), residues: 2051 helix: 3.62 (0.15), residues: 1050 sheet: -0.21 (0.34), residues: 273 loop : -1.62 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 271 TYR 0.013 0.001 TYR A 291 PHE 0.023 0.001 PHE A 148 TRP 0.006 0.001 TRP A 184 HIS 0.003 0.001 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00341 (15561) covalent geometry : angle 0.70569 (20972) hydrogen bonds : bond 0.03348 ( 1090) hydrogen bonds : angle 3.30612 ( 3090) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 254 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8761 (mmtm) REVERT: A 260 GLU cc_start: 0.9275 (tp30) cc_final: 0.8776 (tm-30) REVERT: A 280 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.8687 (tm-30) REVERT: A 315 ASP cc_start: 0.9532 (t0) cc_final: 0.9276 (t0) REVERT: B 145 LEU cc_start: 0.8827 (mt) cc_final: 0.8524 (pp) REVERT: B 260 GLU cc_start: 0.9420 (tp30) cc_final: 0.8812 (tp30) REVERT: C 137 HIS cc_start: 0.8763 (OUTLIER) cc_final: 0.8521 (m90) REVERT: C 140 MET cc_start: 0.7743 (mpm) cc_final: 0.7483 (mpm) REVERT: C 260 GLU cc_start: 0.9395 (tp30) cc_final: 0.8890 (tp30) REVERT: C 280 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8584 (tm-30) REVERT: D 260 GLU cc_start: 0.9336 (tp30) cc_final: 0.9036 (tp30) REVERT: E 250 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8740 (mttp) REVERT: E 260 GLU cc_start: 0.9238 (tp30) cc_final: 0.8576 (tp30) REVERT: E 301 GLU cc_start: 0.9190 (mp0) cc_final: 0.8820 (pm20) REVERT: F 172 MET cc_start: 0.8926 (tmm) cc_final: 0.8477 (tmm) REVERT: F 176 ASP cc_start: 0.7728 (t0) cc_final: 0.6981 (t0) REVERT: F 260 GLU cc_start: 0.9377 (tp30) cc_final: 0.8754 (tp30) REVERT: G 260 GLU cc_start: 0.9381 (tp30) cc_final: 0.8805 (tp30) outliers start: 14 outliers final: 6 residues processed: 258 average time/residue: 0.5853 time to fit residues: 164.8352 Evaluate side-chains 256 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 245 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 136 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 193 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 116 optimal weight: 70.0000 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 40.0000 chunk 199 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.094887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.058295 restraints weight = 37355.701| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 3.00 r_work: 0.2521 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15561 Z= 0.183 Angle : 0.728 11.164 20972 Z= 0.346 Chirality : 0.046 0.261 2443 Planarity : 0.004 0.062 2639 Dihedral : 5.966 57.605 2667 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.07 % Allowed : 26.28 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.19), residues: 2051 helix: 3.65 (0.15), residues: 1050 sheet: -0.22 (0.34), residues: 273 loop : -1.64 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 271 TYR 0.015 0.001 TYR A 291 PHE 0.020 0.001 PHE C 148 TRP 0.008 0.001 TRP A 184 HIS 0.003 0.001 HIS F 320 Details of bonding type rmsd covalent geometry : bond 0.00427 (15561) covalent geometry : angle 0.72756 (20972) hydrogen bonds : bond 0.03650 ( 1090) hydrogen bonds : angle 3.37968 ( 3090) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 247 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8772 (mmtm) REVERT: A 260 GLU cc_start: 0.9290 (tp30) cc_final: 0.8837 (tm-30) REVERT: A 280 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8958 (tt0) REVERT: A 315 ASP cc_start: 0.9536 (t0) cc_final: 0.9276 (t0) REVERT: B 145 LEU cc_start: 0.8803 (mt) cc_final: 0.8525 (pp) REVERT: B 260 GLU cc_start: 0.9424 (tp30) cc_final: 0.8843 (tp30) REVERT: C 137 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8517 (m90) REVERT: C 260 GLU cc_start: 0.9412 (tp30) cc_final: 0.8863 (tp30) REVERT: C 280 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8604 (tm-30) REVERT: D 260 GLU cc_start: 0.9341 (tp30) cc_final: 0.9036 (tp30) REVERT: D 261 MET cc_start: 0.9343 (tmm) cc_final: 0.9090 (tmm) REVERT: E 250 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8776 (mttp) REVERT: E 260 GLU cc_start: 0.9244 (tp30) cc_final: 0.8588 (tp30) REVERT: E 301 GLU cc_start: 0.9209 (mp0) cc_final: 0.8835 (pm20) REVERT: F 172 MET cc_start: 0.8961 (tmm) cc_final: 0.8469 (tmm) REVERT: F 176 ASP cc_start: 0.7799 (t0) cc_final: 0.7047 (t0) REVERT: F 260 GLU cc_start: 0.9384 (tp30) cc_final: 0.8746 (tp30) REVERT: G 260 GLU cc_start: 0.9380 (tp30) cc_final: 0.8812 (tp30) outliers start: 14 outliers final: 8 residues processed: 254 average time/residue: 0.5913 time to fit residues: 164.2110 Evaluate side-chains 256 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 243 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain G residue 137 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 35 optimal weight: 30.0000 chunk 125 optimal weight: 0.0040 chunk 33 optimal weight: 40.0000 chunk 152 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 148 optimal weight: 50.0000 chunk 164 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 60 optimal weight: 60.0000 chunk 118 optimal weight: 60.0000 chunk 122 optimal weight: 6.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.093579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.056797 restraints weight = 37389.612| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 2.96 r_work: 0.2483 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 15561 Z= 0.285 Angle : 0.762 11.059 20972 Z= 0.372 Chirality : 0.048 0.244 2443 Planarity : 0.004 0.064 2639 Dihedral : 6.282 54.046 2667 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.07 % Allowed : 26.59 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.19), residues: 2051 helix: 3.29 (0.15), residues: 1092 sheet: 0.02 (0.35), residues: 245 loop : -1.86 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 271 TYR 0.019 0.001 TYR A 291 PHE 0.023 0.002 PHE A 148 TRP 0.011 0.002 TRP F 184 HIS 0.008 0.002 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00669 (15561) covalent geometry : angle 0.76242 (20972) hydrogen bonds : bond 0.04509 ( 1090) hydrogen bonds : angle 3.60698 ( 3090) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5602.41 seconds wall clock time: 95 minutes 48.82 seconds (5748.82 seconds total)