Starting phenix.real_space_refine on Thu Sep 18 11:14:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oo0_13003/09_2025/7oo0_13003.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oo0_13003/09_2025/7oo0_13003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oo0_13003/09_2025/7oo0_13003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oo0_13003/09_2025/7oo0_13003.map" model { file = "/net/cci-nas-00/data/ceres_data/7oo0_13003/09_2025/7oo0_13003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oo0_13003/09_2025/7oo0_13003.cif" } resolution = 3.1 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= 0.013 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 42 5.16 5 C 10402 2.51 5 N 2450 2.21 5 O 3115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16016 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "B" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "C" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "D" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "E" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "F" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "G" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "A" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 257 Unusual residues: {'LMT': 6, 'PEE': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 327 Unusual residues: {'LMT': 8, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 4.07, per 1000 atoms: 0.25 Number of scatterers: 16016 At special positions: 0 Unit cell: (97.842, 98.9055, 137.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 7 15.00 O 3115 8.00 N 2450 7.00 C 10402 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: 1.26 Conformation dependent library (CDL) restraints added in 678.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 15 sheets defined 56.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 20 through 59 removed outlier: 4.406A pdb=" N LEU A 24 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 89 Processing helix chain 'A' and resid 92 through 128 removed outlier: 5.421A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.539A pdb=" N GLY A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'B' and resid 20 through 59 removed outlier: 4.405A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 89 Processing helix chain 'B' and resid 92 through 128 removed outlier: 5.421A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 removed outlier: 3.540A pdb=" N GLY B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'C' and resid 20 through 59 removed outlier: 4.405A pdb=" N LEU C 24 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 89 Processing helix chain 'C' and resid 92 through 128 removed outlier: 5.420A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 removed outlier: 3.540A pdb=" N GLY C 173 " --> pdb=" O LYS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'D' and resid 20 through 59 removed outlier: 4.405A pdb=" N LEU D 24 " --> pdb=" O ASN D 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 89 Processing helix chain 'D' and resid 92 through 128 removed outlier: 5.421A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 removed outlier: 3.540A pdb=" N GLY D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 245 through 265 Processing helix chain 'E' and resid 20 through 59 removed outlier: 4.406A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 89 Processing helix chain 'E' and resid 92 through 128 removed outlier: 5.421A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 removed outlier: 3.540A pdb=" N GLY E 173 " --> pdb=" O LYS E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 245 through 265 Processing helix chain 'F' and resid 20 through 59 removed outlier: 4.406A pdb=" N LEU F 24 " --> pdb=" O ASN F 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 89 Processing helix chain 'F' and resid 92 through 128 removed outlier: 5.421A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 removed outlier: 3.539A pdb=" N GLY F 173 " --> pdb=" O LYS F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 245 through 265 Processing helix chain 'G' and resid 20 through 59 removed outlier: 4.406A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 89 Processing helix chain 'G' and resid 92 through 128 removed outlier: 5.421A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 173 removed outlier: 3.539A pdb=" N GLY G 173 " --> pdb=" O LYS G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 245 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 166 removed outlier: 7.074A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 176 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.054A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TRP A 240 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET A 221 " --> pdb=" O TRP A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 279 removed outlier: 7.289A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE B 277 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A 278 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ARG B 279 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C 275 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASN B 276 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE C 277 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS B 278 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ARG C 279 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL D 275 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASN C 276 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE D 277 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS C 278 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ARG D 279 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL E 275 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN D 276 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE E 277 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS D 278 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ARG E 279 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL F 275 " --> pdb=" O ASP E 274 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASN E 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE F 277 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS E 278 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ARG F 279 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL G 275 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE G 277 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS F 278 " --> pdb=" O PHE G 277 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ARG G 279 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 275 " --> pdb=" O LYS G 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 162 through 166 removed outlier: 7.074A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 176 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.054A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TRP B 240 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET B 221 " --> pdb=" O TRP B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 162 through 166 removed outlier: 7.074A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 176 " --> pdb=" O ASP C 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.053A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N TRP C 240 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N MET C 221 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 162 through 166 removed outlier: 7.074A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 176 " --> pdb=" O ASP D 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.053A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TRP D 240 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET D 221 " --> pdb=" O TRP D 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 162 through 166 removed outlier: 7.075A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 176 " --> pdb=" O ASP E 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.053A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N TRP E 240 " --> pdb=" O MET E 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET E 221 " --> pdb=" O TRP E 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 162 through 166 removed outlier: 7.075A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE F 176 " --> pdb=" O ASP F 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.053A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TRP F 240 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET F 221 " --> pdb=" O TRP F 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 162 through 166 removed outlier: 7.075A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE G 176 " --> pdb=" O ASP G 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.053A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N TRP G 240 " --> pdb=" O MET G 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET G 221 " --> pdb=" O TRP G 240 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2961 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: 2.64 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2312 1.32 - 1.44: 4180 1.44 - 1.56: 9643 1.56 - 1.68: 14 1.68 - 1.80: 84 Bond restraints: 16233 Sorted by residual: bond pdb=" C4 PEE D 302 " pdb=" O4P PEE D 302 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.15e+00 bond pdb=" C4 PEE E 302 " pdb=" O4P PEE E 302 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C4 PEE F 302 " pdb=" O4P PEE F 302 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C4 PEE B 302 " pdb=" O4P PEE B 302 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 3.98e+00 bond pdb=" C4 PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 3.94e+00 ... (remaining 16228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 21120 2.27 - 4.54: 692 4.54 - 6.82: 28 6.82 - 9.09: 0 9.09 - 11.36: 7 Bond angle restraints: 21847 Sorted by residual: angle pdb=" O3P PEE E 302 " pdb=" P PEE E 302 " pdb=" O4P PEE E 302 " ideal model delta sigma weight residual 92.91 104.27 -11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3P PEE D 302 " pdb=" P PEE D 302 " pdb=" O4P PEE D 302 " ideal model delta sigma weight residual 92.91 104.26 -11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 92.91 104.25 -11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3P PEE F 302 " pdb=" P PEE F 302 " pdb=" O4P PEE F 302 " ideal model delta sigma weight residual 92.91 104.24 -11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3P PEE C 302 " pdb=" P PEE C 302 " pdb=" O4P PEE C 302 " ideal model delta sigma weight residual 92.91 104.24 -11.33 3.00e+00 1.11e-01 1.43e+01 ... (remaining 21842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.61: 10884 30.61 - 61.22: 407 61.22 - 91.84: 147 91.84 - 122.45: 280 122.45 - 153.06: 77 Dihedral angle restraints: 11795 sinusoidal: 6538 harmonic: 5257 Sorted by residual: dihedral pdb=" O2 PEE D 302 " pdb=" C1 PEE D 302 " pdb=" C2 PEE D 302 " pdb=" O3P PEE D 302 " ideal model delta sinusoidal sigma weight residual -59.96 93.10 -153.06 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" O2 PEE F 302 " pdb=" C1 PEE F 302 " pdb=" C2 PEE F 302 " pdb=" O3P PEE F 302 " ideal model delta sinusoidal sigma weight residual -59.96 93.10 -153.06 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" O2 PEE E 302 " pdb=" C1 PEE E 302 " pdb=" C2 PEE E 302 " pdb=" O3P PEE E 302 " ideal model delta sinusoidal sigma weight residual -59.96 93.09 -153.05 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 11792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1715 0.038 - 0.075: 813 0.075 - 0.113: 254 0.113 - 0.151: 53 0.151 - 0.188: 21 Chirality restraints: 2856 Sorted by residual: chirality pdb=" C2 PEE G 404 " pdb=" C1 PEE G 404 " pdb=" C3 PEE G 404 " pdb=" O2 PEE G 404 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" C2 PEE D 302 " pdb=" C1 PEE D 302 " pdb=" C3 PEE D 302 " pdb=" O2 PEE D 302 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" C2 PEE F 302 " pdb=" C1 PEE F 302 " pdb=" C3 PEE F 302 " pdb=" O2 PEE F 302 " both_signs ideal model delta sigma weight residual False -2.33 -2.51 0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 2853 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 83 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C ILE F 83 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE F 83 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA F 84 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 83 " 0.009 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C ILE C 83 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE C 83 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA C 84 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 83 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C ILE A 83 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 83 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A 84 " -0.010 2.00e-02 2.50e+03 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 311 2.68 - 3.24: 15368 3.24 - 3.79: 24084 3.79 - 4.35: 32887 4.35 - 4.90: 56743 Nonbonded interactions: 129393 Sorted by model distance: nonbonded pdb=" O3' LMT B 308 " pdb=" O2B LMT C 308 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR F 27 " pdb=" O2B LMT F 305 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR C 27 " pdb=" O2B LMT C 305 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR D 27 " pdb=" O2B LMT D 305 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR E 27 " pdb=" O2B LMT E 305 " model vdw 2.241 3.040 ... (remaining 129388 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 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'B' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'C' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'D' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'E' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'F' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'G' and (resid 19 through 280 or resid 403 or resid 405 through 407)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.600 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.009 0.041 16233 Z= 0.384 Angle : 0.864 11.360 21847 Z= 0.397 Chirality : 0.049 0.188 2856 Planarity : 0.005 0.030 2450 Dihedral : 28.475 153.060 8407 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.16), residues: 1820 helix: -1.29 (0.10), residues: 1036 sheet: -1.80 (0.25), residues: 273 loop : 0.04 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 219 TYR 0.010 0.002 TYR E 75 PHE 0.012 0.002 PHE B 277 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00879 (16233) covalent geometry : angle 0.86427 (21847) hydrogen bonds : bond 0.12342 ( 994) hydrogen bonds : angle 5.85397 ( 2961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.580 Fit side-chains REVERT: A 128 ARG cc_start: 0.7767 (mmt180) cc_final: 0.7423 (mmt180) REVERT: A 227 GLU cc_start: 0.8357 (tt0) cc_final: 0.7968 (tt0) REVERT: B 128 ARG cc_start: 0.7635 (mmt180) cc_final: 0.7155 (mmt180) REVERT: C 128 ARG cc_start: 0.7845 (mmt180) cc_final: 0.7520 (mmt180) REVERT: C 255 GLU cc_start: 0.7821 (tt0) cc_final: 0.7560 (tt0) REVERT: D 128 ARG cc_start: 0.7634 (mmt180) cc_final: 0.7315 (mmt180) REVERT: D 202 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7667 (mtpt) REVERT: D 227 GLU cc_start: 0.8124 (tt0) cc_final: 0.7904 (tt0) REVERT: E 126 MET cc_start: 0.8160 (mtp) cc_final: 0.7933 (ttm) REVERT: E 128 ARG cc_start: 0.7848 (mmt180) cc_final: 0.7513 (mmt180) REVERT: E 187 GLU cc_start: 0.7938 (tt0) cc_final: 0.7664 (tt0) REVERT: E 221 MET cc_start: 0.8756 (mtm) cc_final: 0.8313 (mtm) REVERT: F 128 ARG cc_start: 0.7686 (mmt180) cc_final: 0.7263 (mmt180) REVERT: G 128 ARG cc_start: 0.7786 (mmt180) cc_final: 0.7420 (mmt180) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1676 time to fit residues: 32.3568 Evaluate side-chains 125 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.139636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.112635 restraints weight = 16987.910| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.69 r_work: 0.3018 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 16233 Z= 0.126 Angle : 0.702 7.226 21847 Z= 0.297 Chirality : 0.054 0.326 2856 Planarity : 0.003 0.022 2450 Dihedral : 26.411 141.631 5278 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.54 % Allowed : 5.05 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.18), residues: 1820 helix: 1.81 (0.14), residues: 1036 sheet: -1.23 (0.26), residues: 308 loop : -0.21 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 219 TYR 0.007 0.001 TYR A 27 PHE 0.009 0.001 PHE C 277 TRP 0.003 0.001 TRP G 240 Details of bonding type rmsd covalent geometry : bond 0.00259 (16233) covalent geometry : angle 0.70198 (21847) hydrogen bonds : bond 0.03989 ( 994) hydrogen bonds : angle 4.00797 ( 2961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.554 Fit side-chains REVERT: A 128 ARG cc_start: 0.7890 (mmt180) cc_final: 0.7467 (mmt180) REVERT: B 128 ARG cc_start: 0.7780 (mmt180) cc_final: 0.7289 (mmt180) REVERT: C 128 ARG cc_start: 0.7989 (mmt180) cc_final: 0.7682 (mmt180) REVERT: C 255 GLU cc_start: 0.8068 (tt0) cc_final: 0.7836 (tt0) REVERT: D 128 ARG cc_start: 0.7854 (mmt180) cc_final: 0.7486 (mmt180) REVERT: D 221 MET cc_start: 0.8444 (mtm) cc_final: 0.8124 (mtm) REVERT: E 221 MET cc_start: 0.8815 (mtm) cc_final: 0.8466 (mtm) REVERT: F 128 ARG cc_start: 0.7667 (mmt180) cc_final: 0.7209 (mmt180) REVERT: F 137 ASP cc_start: 0.8285 (t0) cc_final: 0.8060 (t0) REVERT: G 187 GLU cc_start: 0.8618 (tt0) cc_final: 0.8402 (tt0) outliers start: 8 outliers final: 5 residues processed: 145 average time/residue: 0.1505 time to fit residues: 32.0611 Evaluate side-chains 130 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 112 GLN C 112 GLN D 112 GLN E 112 GLN F 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.136972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109549 restraints weight = 17365.076| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.71 r_work: 0.2978 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16233 Z= 0.183 Angle : 0.788 8.847 21847 Z= 0.322 Chirality : 0.057 0.364 2856 Planarity : 0.003 0.037 2450 Dihedral : 20.200 125.996 5278 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.94 % Allowed : 6.00 % Favored : 93.06 % 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 aren not related in a simple way. whole: 1.58 (0.18), residues: 1820 helix: 2.46 (0.14), residues: 1036 sheet: -0.85 (0.27), residues: 308 loop : -0.80 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 59 TYR 0.007 0.001 TYR A 75 PHE 0.011 0.002 PHE G 277 TRP 0.004 0.001 TRP D 240 Details of bonding type rmsd covalent geometry : bond 0.00439 (16233) covalent geometry : angle 0.78778 (21847) hydrogen bonds : bond 0.04201 ( 994) hydrogen bonds : angle 3.95019 ( 2961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.578 Fit side-chains REVERT: A 128 ARG cc_start: 0.7854 (mmt180) cc_final: 0.7470 (mmt180) REVERT: A 227 GLU cc_start: 0.8647 (tt0) cc_final: 0.8386 (tt0) REVERT: B 128 ARG cc_start: 0.7781 (mmt180) cc_final: 0.7322 (mmt180) REVERT: C 128 ARG cc_start: 0.8019 (mmt180) cc_final: 0.7720 (mmt180) REVERT: D 128 ARG cc_start: 0.7773 (mmt180) cc_final: 0.7472 (mmt180) REVERT: D 221 MET cc_start: 0.8476 (mtm) cc_final: 0.8158 (mtm) REVERT: E 128 ARG cc_start: 0.7981 (mmt180) cc_final: 0.7450 (mmt180) REVERT: E 221 MET cc_start: 0.8861 (mtm) cc_final: 0.8512 (mtm) REVERT: F 128 ARG cc_start: 0.7671 (mmt180) cc_final: 0.7238 (mmt180) REVERT: F 137 ASP cc_start: 0.8316 (t0) cc_final: 0.8103 (t0) REVERT: G 187 GLU cc_start: 0.8652 (tt0) cc_final: 0.8435 (tt0) outliers start: 14 outliers final: 10 residues processed: 151 average time/residue: 0.1490 time to fit residues: 32.8713 Evaluate side-chains 147 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 57 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.138523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.110484 restraints weight = 17113.774| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.76 r_work: 0.2995 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16233 Z= 0.150 Angle : 0.706 8.283 21847 Z= 0.292 Chirality : 0.054 0.398 2856 Planarity : 0.003 0.046 2450 Dihedral : 17.573 123.130 5278 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.88 % Allowed : 7.55 % Favored : 91.58 % 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 aren not related in a simple way. whole: 1.89 (0.19), residues: 1820 helix: 2.79 (0.15), residues: 1036 sheet: -0.57 (0.27), residues: 308 loop : -1.01 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 59 TYR 0.005 0.001 TYR F 75 PHE 0.009 0.001 PHE G 277 TRP 0.002 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00348 (16233) covalent geometry : angle 0.70560 (21847) hydrogen bonds : bond 0.03824 ( 994) hydrogen bonds : angle 3.79349 ( 2961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.563 Fit side-chains REVERT: A 128 ARG cc_start: 0.7792 (mmt180) cc_final: 0.7399 (mmt180) REVERT: A 227 GLU cc_start: 0.8555 (tt0) cc_final: 0.8275 (tt0) REVERT: B 58 SER cc_start: 0.7328 (t) cc_final: 0.7117 (t) REVERT: B 128 ARG cc_start: 0.7800 (mmt180) cc_final: 0.7295 (mmt180) REVERT: B 137 ASP cc_start: 0.8389 (t0) cc_final: 0.8189 (t0) REVERT: C 128 ARG cc_start: 0.7920 (mmt180) cc_final: 0.7636 (mmt180) REVERT: D 128 ARG cc_start: 0.7725 (mmt180) cc_final: 0.7425 (mmt180) REVERT: D 221 MET cc_start: 0.8406 (mtm) cc_final: 0.8186 (mtm) REVERT: E 128 ARG cc_start: 0.7934 (mmt180) cc_final: 0.7401 (mmt180) REVERT: E 221 MET cc_start: 0.8804 (mtm) cc_final: 0.8477 (mtm) REVERT: F 128 ARG cc_start: 0.7636 (mmt180) cc_final: 0.7200 (mmt180) REVERT: G 187 GLU cc_start: 0.8674 (tt0) cc_final: 0.8456 (tt0) outliers start: 13 outliers final: 7 residues processed: 159 average time/residue: 0.1526 time to fit residues: 35.4815 Evaluate side-chains 151 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 8 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.140127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.112117 restraints weight = 17008.756| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.75 r_work: 0.3014 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16233 Z= 0.119 Angle : 0.633 7.554 21847 Z= 0.267 Chirality : 0.050 0.351 2856 Planarity : 0.003 0.054 2450 Dihedral : 16.754 120.017 5278 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 1.08 % Allowed : 8.63 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.19), residues: 1820 helix: 3.07 (0.15), residues: 1036 sheet: -0.39 (0.27), residues: 308 loop : -1.07 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 59 TYR 0.004 0.001 TYR F 75 PHE 0.008 0.001 PHE G 277 TRP 0.002 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00265 (16233) covalent geometry : angle 0.63273 (21847) hydrogen bonds : bond 0.03562 ( 994) hydrogen bonds : angle 3.66981 ( 2961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.466 Fit side-chains REVERT: A 128 ARG cc_start: 0.7745 (mmt180) cc_final: 0.7330 (mmt180) REVERT: A 227 GLU cc_start: 0.8570 (tt0) cc_final: 0.8301 (tt0) REVERT: B 58 SER cc_start: 0.7198 (t) cc_final: 0.6981 (t) REVERT: B 128 ARG cc_start: 0.7718 (mmt180) cc_final: 0.7240 (mmt180) REVERT: C 128 ARG cc_start: 0.7882 (mmt180) cc_final: 0.7573 (mmt180) REVERT: D 128 ARG cc_start: 0.7617 (mmt180) cc_final: 0.7260 (mmt180) REVERT: D 221 MET cc_start: 0.8388 (mtm) cc_final: 0.8183 (mtm) REVERT: E 128 ARG cc_start: 0.7902 (mmt180) cc_final: 0.7382 (mmt180) REVERT: E 221 MET cc_start: 0.8762 (mtm) cc_final: 0.8441 (mtm) REVERT: F 128 ARG cc_start: 0.7596 (mmt180) cc_final: 0.7158 (mmt180) REVERT: G 187 GLU cc_start: 0.8691 (tt0) cc_final: 0.8484 (tt0) outliers start: 16 outliers final: 10 residues processed: 166 average time/residue: 0.1442 time to fit residues: 35.0341 Evaluate side-chains 156 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 149 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 180 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 120 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.141475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.114034 restraints weight = 16955.863| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.67 r_work: 0.3036 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 16233 Z= 0.111 Angle : 0.604 6.701 21847 Z= 0.257 Chirality : 0.048 0.328 2856 Planarity : 0.003 0.057 2450 Dihedral : 16.185 119.817 5278 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.15 % Allowed : 8.76 % Favored : 90.09 % 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 aren not related in a simple way. whole: 2.40 (0.19), residues: 1820 helix: 3.26 (0.14), residues: 1036 sheet: -0.29 (0.27), residues: 308 loop : -1.03 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 59 TYR 0.003 0.001 TYR B 250 PHE 0.008 0.001 PHE D 188 TRP 0.002 0.000 TRP A 240 Details of bonding type rmsd covalent geometry : bond 0.00243 (16233) covalent geometry : angle 0.60416 (21847) hydrogen bonds : bond 0.03409 ( 994) hydrogen bonds : angle 3.59185 ( 2961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.557 Fit side-chains REVERT: A 128 ARG cc_start: 0.7829 (mmt180) cc_final: 0.7401 (mmt180) REVERT: A 137 ASP cc_start: 0.8261 (t70) cc_final: 0.7981 (t0) REVERT: A 227 GLU cc_start: 0.8570 (tt0) cc_final: 0.8299 (tt0) REVERT: B 58 SER cc_start: 0.7309 (t) cc_final: 0.7081 (t) REVERT: B 128 ARG cc_start: 0.7813 (mmt180) cc_final: 0.7347 (mmt180) REVERT: C 128 ARG cc_start: 0.7893 (mmt180) cc_final: 0.7592 (mmt180) REVERT: D 24 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6712 (mp) REVERT: D 128 ARG cc_start: 0.7662 (mmt180) cc_final: 0.7283 (mmt180) REVERT: D 221 MET cc_start: 0.8398 (mtm) cc_final: 0.8192 (mtm) REVERT: E 128 ARG cc_start: 0.7954 (mmt180) cc_final: 0.7483 (mmt180) REVERT: E 221 MET cc_start: 0.8771 (mtm) cc_final: 0.8452 (mtm) REVERT: F 128 ARG cc_start: 0.7643 (mmt180) cc_final: 0.7240 (mmt180) REVERT: G 187 GLU cc_start: 0.8741 (tt0) cc_final: 0.8526 (tt0) outliers start: 17 outliers final: 10 residues processed: 170 average time/residue: 0.1431 time to fit residues: 35.7964 Evaluate side-chains 160 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 106 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 108 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.141604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.114160 restraints weight = 16905.204| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.67 r_work: 0.3041 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 16233 Z= 0.112 Angle : 0.598 6.641 21847 Z= 0.255 Chirality : 0.048 0.317 2856 Planarity : 0.003 0.053 2450 Dihedral : 15.909 118.449 5278 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.21 % Allowed : 8.89 % Favored : 89.89 % 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 aren not related in a simple way. whole: 2.45 (0.19), residues: 1820 helix: 3.30 (0.14), residues: 1036 sheet: -0.23 (0.26), residues: 308 loop : -1.03 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 59 TYR 0.003 0.001 TYR F 75 PHE 0.009 0.001 PHE F 188 TRP 0.002 0.001 TRP A 240 Details of bonding type rmsd covalent geometry : bond 0.00248 (16233) covalent geometry : angle 0.59797 (21847) hydrogen bonds : bond 0.03408 ( 994) hydrogen bonds : angle 3.58212 ( 2961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.339 Fit side-chains REVERT: A 24 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6781 (mp) REVERT: A 128 ARG cc_start: 0.7838 (mmt180) cc_final: 0.7422 (mmt180) REVERT: A 137 ASP cc_start: 0.8276 (t70) cc_final: 0.7999 (t0) REVERT: A 227 GLU cc_start: 0.8574 (tt0) cc_final: 0.8305 (tt0) REVERT: B 24 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6714 (mp) REVERT: B 58 SER cc_start: 0.7286 (t) cc_final: 0.7059 (t) REVERT: B 128 ARG cc_start: 0.7819 (mmt180) cc_final: 0.7355 (mmt180) REVERT: C 24 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6895 (mp) REVERT: C 128 ARG cc_start: 0.7851 (mmt180) cc_final: 0.7559 (mmt180) REVERT: D 128 ARG cc_start: 0.7682 (mmt180) cc_final: 0.7312 (mmt180) REVERT: E 128 ARG cc_start: 0.7888 (mmt180) cc_final: 0.7427 (mmt180) REVERT: E 221 MET cc_start: 0.8765 (mtm) cc_final: 0.8445 (mtm) REVERT: F 128 ARG cc_start: 0.7675 (mmt180) cc_final: 0.7266 (mmt180) REVERT: G 187 GLU cc_start: 0.8759 (tt0) cc_final: 0.8547 (tt0) outliers start: 18 outliers final: 11 residues processed: 168 average time/residue: 0.1240 time to fit residues: 30.7436 Evaluate side-chains 164 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 106 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.139507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.111888 restraints weight = 17137.422| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.67 r_work: 0.3008 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 16233 Z= 0.154 Angle : 0.634 7.338 21847 Z= 0.272 Chirality : 0.049 0.347 2856 Planarity : 0.003 0.056 2450 Dihedral : 15.818 116.865 5278 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.42 % Allowed : 8.83 % Favored : 89.76 % 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 aren not related in a simple way. whole: 2.25 (0.19), residues: 1820 helix: 3.09 (0.15), residues: 1036 sheet: -0.17 (0.27), residues: 308 loop : -1.10 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 59 TYR 0.006 0.001 TYR C 75 PHE 0.011 0.001 PHE F 188 TRP 0.003 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00368 (16233) covalent geometry : angle 0.63422 (21847) hydrogen bonds : bond 0.03715 ( 994) hydrogen bonds : angle 3.71569 ( 2961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.662 Fit side-chains REVERT: A 24 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6989 (mp) REVERT: A 128 ARG cc_start: 0.7831 (mmt180) cc_final: 0.7445 (mmt180) REVERT: A 227 GLU cc_start: 0.8556 (tt0) cc_final: 0.8301 (tt0) REVERT: B 58 SER cc_start: 0.7288 (t) cc_final: 0.7056 (t) REVERT: B 128 ARG cc_start: 0.7812 (mmt180) cc_final: 0.7365 (mmt180) REVERT: C 24 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6931 (mp) REVERT: C 128 ARG cc_start: 0.7861 (mmt180) cc_final: 0.7556 (mmt180) REVERT: D 24 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6719 (mp) REVERT: D 128 ARG cc_start: 0.7689 (mmt180) cc_final: 0.7398 (mmt180) REVERT: E 128 ARG cc_start: 0.7911 (mmt180) cc_final: 0.7397 (mmt180) REVERT: E 221 MET cc_start: 0.8819 (mtm) cc_final: 0.8513 (mtm) REVERT: F 128 ARG cc_start: 0.7649 (mmt180) cc_final: 0.7247 (mmt180) REVERT: G 187 GLU cc_start: 0.8776 (tt0) cc_final: 0.8567 (tt0) outliers start: 21 outliers final: 12 residues processed: 169 average time/residue: 0.1328 time to fit residues: 33.1253 Evaluate side-chains 162 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 125 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 63 optimal weight: 0.0060 chunk 159 optimal weight: 1.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.139339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.111563 restraints weight = 17109.084| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.68 r_work: 0.3007 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 16233 Z= 0.154 Angle : 0.636 6.750 21847 Z= 0.274 Chirality : 0.049 0.377 2856 Planarity : 0.003 0.059 2450 Dihedral : 15.601 113.932 5278 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.21 % Allowed : 9.10 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.19), residues: 1820 helix: 3.07 (0.14), residues: 1036 sheet: -0.08 (0.27), residues: 308 loop : -1.17 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 59 TYR 0.006 0.001 TYR B 250 PHE 0.011 0.001 PHE F 188 TRP 0.004 0.001 TRP A 240 Details of bonding type rmsd covalent geometry : bond 0.00368 (16233) covalent geometry : angle 0.63600 (21847) hydrogen bonds : bond 0.03759 ( 994) hydrogen bonds : angle 3.73289 ( 2961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.471 Fit side-chains REVERT: A 24 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7008 (mp) REVERT: A 56 MET cc_start: 0.7607 (mtm) cc_final: 0.7368 (mtm) REVERT: A 128 ARG cc_start: 0.7870 (mmt180) cc_final: 0.7475 (mmt180) REVERT: A 137 ASP cc_start: 0.8300 (t70) cc_final: 0.8050 (t0) REVERT: A 227 GLU cc_start: 0.8570 (tt0) cc_final: 0.8316 (tt0) REVERT: B 58 SER cc_start: 0.7418 (t) cc_final: 0.7215 (t) REVERT: B 128 ARG cc_start: 0.7818 (mmt180) cc_final: 0.7391 (mmt180) REVERT: C 24 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6903 (mp) REVERT: C 128 ARG cc_start: 0.7928 (mmt180) cc_final: 0.7662 (mmt180) REVERT: D 24 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6681 (mp) REVERT: D 128 ARG cc_start: 0.7843 (mmt180) cc_final: 0.7544 (mmt180) REVERT: E 128 ARG cc_start: 0.7893 (mmt180) cc_final: 0.7367 (mmt180) REVERT: E 221 MET cc_start: 0.8803 (mtm) cc_final: 0.8541 (mtm) REVERT: F 128 ARG cc_start: 0.7701 (mmt180) cc_final: 0.7329 (mmt180) outliers start: 18 outliers final: 10 residues processed: 165 average time/residue: 0.1416 time to fit residues: 34.3914 Evaluate side-chains 160 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 70 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 99 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.142323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.114652 restraints weight = 16830.587| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.67 r_work: 0.3047 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16233 Z= 0.104 Angle : 0.591 7.614 21847 Z= 0.254 Chirality : 0.047 0.347 2856 Planarity : 0.003 0.056 2450 Dihedral : 15.065 112.870 5278 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.67 % Allowed : 9.70 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.19), residues: 1820 helix: 3.35 (0.14), residues: 1036 sheet: -0.04 (0.27), residues: 308 loop : -1.13 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 59 TYR 0.003 0.001 TYR F 75 PHE 0.010 0.001 PHE F 188 TRP 0.002 0.000 TRP A 240 Details of bonding type rmsd covalent geometry : bond 0.00221 (16233) covalent geometry : angle 0.59124 (21847) hydrogen bonds : bond 0.03321 ( 994) hydrogen bonds : angle 3.54320 ( 2961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.535 Fit side-chains REVERT: A 24 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6847 (mp) REVERT: A 128 ARG cc_start: 0.7841 (mmt180) cc_final: 0.7432 (mmt180) REVERT: A 137 ASP cc_start: 0.8304 (t70) cc_final: 0.8043 (t0) REVERT: A 227 GLU cc_start: 0.8563 (tt0) cc_final: 0.8293 (tt0) REVERT: B 128 ARG cc_start: 0.7810 (mmt180) cc_final: 0.7350 (mmt180) REVERT: C 128 ARG cc_start: 0.7886 (mmt180) cc_final: 0.7573 (mmt180) REVERT: C 181 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8395 (mm-30) REVERT: D 24 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6649 (mp) REVERT: D 128 ARG cc_start: 0.7697 (mmt180) cc_final: 0.7417 (mmt180) REVERT: E 128 ARG cc_start: 0.7896 (mmt180) cc_final: 0.7385 (mmt180) REVERT: E 221 MET cc_start: 0.8729 (mtm) cc_final: 0.8476 (mtm) REVERT: F 128 ARG cc_start: 0.7640 (mmt180) cc_final: 0.7238 (mmt180) outliers start: 10 outliers final: 6 residues processed: 163 average time/residue: 0.1389 time to fit residues: 33.4467 Evaluate side-chains 159 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 125 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.138148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109710 restraints weight = 17118.782| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.77 r_work: 0.2985 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 16233 Z= 0.188 Angle : 0.662 7.724 21847 Z= 0.287 Chirality : 0.050 0.378 2856 Planarity : 0.003 0.060 2450 Dihedral : 14.990 111.828 5278 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.35 % Allowed : 9.23 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.18), residues: 1820 helix: 2.96 (0.15), residues: 1036 sheet: 0.30 (0.28), residues: 245 loop : -1.32 (0.22), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 59 TYR 0.007 0.001 TYR B 250 PHE 0.012 0.002 PHE G 188 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00457 (16233) covalent geometry : angle 0.66248 (21847) hydrogen bonds : bond 0.03943 ( 994) hydrogen bonds : angle 3.80344 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3581.25 seconds wall clock time: 62 minutes 26.02 seconds (3746.02 seconds total)