Starting phenix.real_space_refine on Tue Dec 31 17:48:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oo0_13003/12_2024/7oo0_13003.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oo0_13003/12_2024/7oo0_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_13003/12_2024/7oo0_13003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oo0_13003/12_2024/7oo0_13003.map" model { file = "/net/cci-nas-00/data/ceres_data/7oo0_13003/12_2024/7oo0_13003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oo0_13003/12_2024/7oo0_13003.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 10.00, per 1000 atoms: 0.62 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: 4.33 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.71 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: 5.14 Time building geometry restraints manager: 4.90 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: 0.950 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: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 36.970 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.080 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.770 ------------------------------------------------------------------------------- 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= 0.548 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 : 7.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (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 TRP 0.004 0.001 TRP F 240 PHE 0.012 0.002 PHE B 277 TYR 0.010 0.002 TYR E 75 ARG 0.004 0.001 ARG D 219 *********************** 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 : 1.637 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 128 ARG cc_start: 0.7848 (mmt180) cc_final: 0.7514 (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: 0.7264 (mmt180) REVERT: G 128 ARG cc_start: 0.7786 (mmt180) cc_final: 0.7421 (mmt180) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3661 time to fit residues: 70.8905 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 : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16233 Z= 0.173 Angle : 0.718 7.151 21847 Z= 0.301 Chirality : 0.055 0.318 2856 Planarity : 0.003 0.021 2450 Dihedral : 25.905 140.802 5278 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.18), residues: 1820 helix: 1.84 (0.14), residues: 1036 sheet: -1.19 (0.28), residues: 273 loop : -0.44 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 240 PHE 0.008 0.001 PHE C 277 TYR 0.007 0.001 TYR E 27 ARG 0.002 0.000 ARG B 224 *********************** 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 148 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 1.602 Fit side-chains REVERT: A 128 ARG cc_start: 0.7615 (mmt180) cc_final: 0.7175 (mmt180) REVERT: B 128 ARG cc_start: 0.7457 (mmt180) cc_final: 0.6901 (mmt180) REVERT: C 128 ARG cc_start: 0.7707 (mmt180) cc_final: 0.7378 (mmt180) REVERT: C 255 GLU cc_start: 0.7703 (tt0) cc_final: 0.7500 (tt0) REVERT: D 128 ARG cc_start: 0.7545 (mmt180) cc_final: 0.7174 (mmt180) REVERT: E 128 ARG cc_start: 0.7665 (mmt180) cc_final: 0.7367 (mmt180) REVERT: E 187 GLU cc_start: 0.7998 (tt0) cc_final: 0.7746 (tt0) REVERT: E 221 MET cc_start: 0.8615 (mtm) cc_final: 0.8245 (mtm) REVERT: F 128 ARG cc_start: 0.7286 (mmt180) cc_final: 0.6818 (mmt180) REVERT: G 128 ARG cc_start: 0.7587 (mmt180) cc_final: 0.7365 (mmt180) REVERT: G 187 GLU cc_start: 0.7981 (tt0) cc_final: 0.7712 (tt0) outliers start: 8 outliers final: 5 residues processed: 147 average time/residue: 0.3067 time to fit residues: 66.8245 Evaluate side-chains 132 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 91 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 F 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16233 Z= 0.195 Angle : 0.756 8.453 21847 Z= 0.305 Chirality : 0.056 0.374 2856 Planarity : 0.002 0.035 2450 Dihedral : 19.447 127.315 5278 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.61 % Allowed : 6.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.18), residues: 1820 helix: 2.57 (0.14), residues: 1036 sheet: -0.90 (0.27), residues: 308 loop : -0.72 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 240 PHE 0.008 0.001 PHE G 277 TYR 0.005 0.001 TYR F 75 ARG 0.008 0.000 ARG B 59 *********************** 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 153 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 1.647 Fit side-chains REVERT: A 128 ARG cc_start: 0.7595 (mmt180) cc_final: 0.7161 (mmt180) REVERT: A 137 ASP cc_start: 0.8059 (t0) cc_final: 0.7814 (t70) REVERT: A 227 GLU cc_start: 0.8075 (tt0) cc_final: 0.7718 (tt0) REVERT: B 128 ARG cc_start: 0.7492 (mmt180) cc_final: 0.6959 (mmt180) REVERT: C 128 ARG cc_start: 0.7710 (mmt180) cc_final: 0.7377 (mmt180) REVERT: D 128 ARG cc_start: 0.7454 (mmt180) cc_final: 0.7085 (mmt180) REVERT: E 128 ARG cc_start: 0.7649 (mmt180) cc_final: 0.7359 (mmt180) REVERT: E 187 GLU cc_start: 0.7985 (tt0) cc_final: 0.7737 (tt0) REVERT: E 221 MET cc_start: 0.8597 (mtm) cc_final: 0.8260 (mtm) REVERT: F 128 ARG cc_start: 0.7404 (mmt180) cc_final: 0.6979 (mmt180) REVERT: G 187 GLU cc_start: 0.7996 (tt0) cc_final: 0.7747 (tt0) outliers start: 9 outliers final: 7 residues processed: 152 average time/residue: 0.3040 time to fit residues: 68.0313 Evaluate side-chains 145 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE 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 163 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 16233 Z= 0.165 Angle : 0.664 8.391 21847 Z= 0.274 Chirality : 0.052 0.387 2856 Planarity : 0.002 0.043 2450 Dihedral : 17.128 124.369 5278 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.81 % Allowed : 7.88 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.19), residues: 1820 helix: 3.05 (0.15), residues: 1036 sheet: -0.64 (0.27), residues: 308 loop : -0.87 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 240 PHE 0.007 0.001 PHE G 277 TYR 0.003 0.001 TYR A 75 ARG 0.013 0.000 ARG E 59 *********************** 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 156 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.531 Fit side-chains REVERT: A 128 ARG cc_start: 0.7554 (mmt180) cc_final: 0.7152 (mmt180) REVERT: A 227 GLU cc_start: 0.8003 (tt0) cc_final: 0.7661 (tt0) REVERT: B 128 ARG cc_start: 0.7485 (mmt180) cc_final: 0.6982 (mmt180) REVERT: C 128 ARG cc_start: 0.7653 (mmt180) cc_final: 0.7340 (mmt180) REVERT: D 128 ARG cc_start: 0.7384 (mmt180) cc_final: 0.6989 (mmt180) REVERT: E 128 ARG cc_start: 0.7616 (mmt180) cc_final: 0.7330 (mmt180) REVERT: E 187 GLU cc_start: 0.8029 (tt0) cc_final: 0.7784 (tt0) REVERT: E 221 MET cc_start: 0.8538 (mtm) cc_final: 0.8239 (mtm) REVERT: F 128 ARG cc_start: 0.7387 (mmt180) cc_final: 0.6965 (mmt180) REVERT: G 187 GLU cc_start: 0.8042 (tt0) cc_final: 0.7772 (tt0) outliers start: 12 outliers final: 5 residues processed: 151 average time/residue: 0.3121 time to fit residues: 69.2745 Evaluate side-chains 147 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16233 Z= 0.349 Angle : 0.727 8.043 21847 Z= 0.312 Chirality : 0.053 0.370 2856 Planarity : 0.004 0.060 2450 Dihedral : 16.859 119.158 5278 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.15 % Allowed : 8.15 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.19), residues: 1820 helix: 2.68 (0.15), residues: 1036 sheet: -0.50 (0.27), residues: 308 loop : -1.08 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 240 PHE 0.012 0.002 PHE G 277 TYR 0.008 0.002 TYR B 250 ARG 0.010 0.001 ARG E 59 *********************** 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 162 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.653 Fit side-chains REVERT: A 128 ARG cc_start: 0.7588 (mmt180) cc_final: 0.7208 (mmt180) REVERT: A 227 GLU cc_start: 0.8012 (tt0) cc_final: 0.7676 (tt0) REVERT: B 128 ARG cc_start: 0.7469 (mmt180) cc_final: 0.6972 (mmt180) REVERT: C 128 ARG cc_start: 0.7683 (mmt180) cc_final: 0.7376 (mmt180) REVERT: C 255 GLU cc_start: 0.7873 (tt0) cc_final: 0.7589 (tt0) REVERT: D 128 ARG cc_start: 0.7474 (mmt180) cc_final: 0.7130 (mmt180) REVERT: D 137 ASP cc_start: 0.8081 (t0) cc_final: 0.7855 (t70) REVERT: E 128 ARG cc_start: 0.7460 (mmt180) cc_final: 0.7156 (mmt180) REVERT: E 187 GLU cc_start: 0.8017 (tt0) cc_final: 0.7727 (tt0) REVERT: E 221 MET cc_start: 0.8705 (mtm) cc_final: 0.8369 (mtm) REVERT: F 128 ARG cc_start: 0.7378 (mmt180) cc_final: 0.6971 (mmt180) REVERT: G 187 GLU cc_start: 0.8065 (tt0) cc_final: 0.7780 (tt0) outliers start: 17 outliers final: 12 residues processed: 159 average time/residue: 0.3187 time to fit residues: 74.5568 Evaluate side-chains 156 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 176 optimal weight: 0.7980 chunk 146 optimal weight: 0.0770 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1998 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= 0.151 Angle : 0.614 7.233 21847 Z= 0.262 Chirality : 0.049 0.341 2856 Planarity : 0.003 0.054 2450 Dihedral : 16.312 119.225 5278 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.74 % Allowed : 9.30 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.19), residues: 1820 helix: 3.14 (0.15), residues: 1036 sheet: -0.36 (0.27), residues: 308 loop : -1.10 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 240 PHE 0.008 0.001 PHE G 188 TYR 0.003 0.001 TYR B 250 ARG 0.010 0.000 ARG E 59 *********************** 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 161 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 2.388 Fit side-chains REVERT: A 128 ARG cc_start: 0.7551 (mmt180) cc_final: 0.7162 (mmt180) REVERT: A 227 GLU cc_start: 0.8009 (tt0) cc_final: 0.7667 (tt0) REVERT: B 128 ARG cc_start: 0.7488 (mmt180) cc_final: 0.6973 (mmt180) REVERT: C 128 ARG cc_start: 0.7648 (mmt180) cc_final: 0.7330 (mmt180) REVERT: D 128 ARG cc_start: 0.7363 (mmt180) cc_final: 0.7020 (mmt180) REVERT: D 137 ASP cc_start: 0.8046 (t0) cc_final: 0.7811 (t70) REVERT: E 128 ARG cc_start: 0.7502 (mmt180) cc_final: 0.7194 (mmt180) REVERT: E 187 GLU cc_start: 0.8062 (tt0) cc_final: 0.7796 (tt0) REVERT: E 221 MET cc_start: 0.8545 (mtm) cc_final: 0.8272 (mtm) REVERT: F 128 ARG cc_start: 0.7365 (mmt180) cc_final: 0.6948 (mmt180) REVERT: G 187 GLU cc_start: 0.8052 (tt0) cc_final: 0.7794 (tt0) outliers start: 11 outliers final: 6 residues processed: 161 average time/residue: 0.3220 time to fit residues: 76.4374 Evaluate side-chains 152 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASN 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 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 169 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 175 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16233 Z= 0.266 Angle : 0.651 7.064 21847 Z= 0.279 Chirality : 0.050 0.342 2856 Planarity : 0.003 0.055 2450 Dihedral : 16.229 118.238 5278 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.28 % Allowed : 8.76 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 1820 helix: 2.98 (0.15), residues: 1036 sheet: -0.26 (0.26), residues: 308 loop : -1.16 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 240 PHE 0.010 0.001 PHE F 188 TYR 0.006 0.001 TYR B 250 ARG 0.010 0.001 ARG E 59 *********************** 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 168 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.645 Fit side-chains REVERT: A 128 ARG cc_start: 0.7555 (mmt180) cc_final: 0.7177 (mmt180) REVERT: A 227 GLU cc_start: 0.8021 (tt0) cc_final: 0.7687 (tt0) REVERT: B 128 ARG cc_start: 0.7506 (mmt180) cc_final: 0.7009 (mmt180) REVERT: C 24 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7207 (mp) REVERT: C 128 ARG cc_start: 0.7678 (mmt180) cc_final: 0.7372 (mmt180) REVERT: D 128 ARG cc_start: 0.7359 (mmt180) cc_final: 0.7001 (mmt180) REVERT: E 128 ARG cc_start: 0.7496 (mmt180) cc_final: 0.7175 (mmt180) REVERT: E 187 GLU cc_start: 0.8049 (tt0) cc_final: 0.7762 (tt0) REVERT: E 221 MET cc_start: 0.8637 (mtm) cc_final: 0.8306 (mtm) REVERT: F 128 ARG cc_start: 0.7398 (mmt180) cc_final: 0.6999 (mmt180) REVERT: G 187 GLU cc_start: 0.8138 (tt0) cc_final: 0.7860 (tt0) outliers start: 19 outliers final: 9 residues processed: 167 average time/residue: 0.3029 time to fit residues: 74.8275 Evaluate side-chains 155 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN 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 108 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16233 Z= 0.211 Angle : 0.634 6.979 21847 Z= 0.271 Chirality : 0.049 0.332 2856 Planarity : 0.003 0.059 2450 Dihedral : 16.085 117.511 5278 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.15 % Allowed : 9.03 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.19), residues: 1820 helix: 3.04 (0.15), residues: 1036 sheet: -0.21 (0.26), residues: 308 loop : -1.16 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 240 PHE 0.010 0.001 PHE F 188 TYR 0.005 0.001 TYR B 250 ARG 0.010 0.000 ARG E 59 *********************** 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 170 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.564 Fit side-chains REVERT: A 24 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7078 (mp) REVERT: A 128 ARG cc_start: 0.7608 (mmt180) cc_final: 0.7213 (mmt180) REVERT: A 227 GLU cc_start: 0.8004 (tt0) cc_final: 0.7665 (tt0) REVERT: B 128 ARG cc_start: 0.7522 (mmt180) cc_final: 0.7041 (mmt180) REVERT: C 128 ARG cc_start: 0.7618 (mmt180) cc_final: 0.7301 (mmt180) REVERT: D 128 ARG cc_start: 0.7376 (mmt180) cc_final: 0.7021 (mmt180) REVERT: E 128 ARG cc_start: 0.7491 (mmt180) cc_final: 0.7174 (mmt180) REVERT: E 187 GLU cc_start: 0.8052 (tt0) cc_final: 0.7773 (tt0) REVERT: E 221 MET cc_start: 0.8591 (mtm) cc_final: 0.8291 (mtm) REVERT: F 128 ARG cc_start: 0.7389 (mmt180) cc_final: 0.6983 (mmt180) REVERT: G 187 GLU cc_start: 0.8130 (tt0) cc_final: 0.7862 (tt0) outliers start: 17 outliers final: 11 residues processed: 169 average time/residue: 0.3043 time to fit residues: 75.9974 Evaluate side-chains 162 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 1.682 ------------------------------------------------------------------------------- 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 B residue 30 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2232 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= 0.167 Angle : 0.603 7.389 21847 Z= 0.258 Chirality : 0.048 0.382 2856 Planarity : 0.003 0.055 2450 Dihedral : 15.617 116.167 5278 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.08 % Allowed : 8.96 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.19), residues: 1820 helix: 3.22 (0.14), residues: 1036 sheet: -0.11 (0.26), residues: 308 loop : -1.15 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 240 PHE 0.009 0.001 PHE F 188 TYR 0.007 0.001 TYR C 27 ARG 0.009 0.000 ARG E 59 *********************** 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 171 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.593 Fit side-chains REVERT: A 24 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.7026 (mp) REVERT: A 128 ARG cc_start: 0.7635 (mmt180) cc_final: 0.7227 (mmt180) REVERT: A 137 ASP cc_start: 0.7683 (t70) cc_final: 0.7446 (t0) REVERT: A 227 GLU cc_start: 0.7998 (tt0) cc_final: 0.7663 (tt0) REVERT: B 128 ARG cc_start: 0.7540 (mmt180) cc_final: 0.7050 (mmt180) REVERT: C 128 ARG cc_start: 0.7658 (mmt180) cc_final: 0.7325 (mmt180) REVERT: D 59 ARG cc_start: 0.7345 (mtt-85) cc_final: 0.7018 (mtt-85) REVERT: D 128 ARG cc_start: 0.7394 (mmt180) cc_final: 0.7037 (mmt180) REVERT: E 128 ARG cc_start: 0.7561 (mmt180) cc_final: 0.7236 (mmt180) REVERT: E 187 GLU cc_start: 0.8074 (tt0) cc_final: 0.7802 (tt0) REVERT: E 221 MET cc_start: 0.8538 (mtm) cc_final: 0.8272 (mtm) REVERT: F 128 ARG cc_start: 0.7380 (mmt180) cc_final: 0.6968 (mmt180) REVERT: G 187 GLU cc_start: 0.8143 (tt0) cc_final: 0.7876 (tt0) outliers start: 16 outliers final: 10 residues processed: 170 average time/residue: 0.2960 time to fit residues: 74.8172 Evaluate side-chains 163 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 29 VAL 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 107 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 181 optimal weight: 0.0980 chunk 166 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 111 optimal weight: 0.2980 chunk 88 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16233 Z= 0.141 Angle : 0.586 7.393 21847 Z= 0.251 Chirality : 0.047 0.335 2856 Planarity : 0.003 0.055 2450 Dihedral : 14.880 113.997 5278 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.74 % Allowed : 9.43 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.19), residues: 1820 helix: 3.43 (0.14), residues: 1036 sheet: -0.05 (0.27), residues: 308 loop : -1.13 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 251 PHE 0.008 0.001 PHE F 188 TYR 0.003 0.001 TYR C 75 ARG 0.010 0.000 ARG E 59 ********************** 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 167 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 1.609 Fit side-chains REVERT: A 128 ARG cc_start: 0.7624 (mmt180) cc_final: 0.7242 (mmt180) REVERT: A 137 ASP cc_start: 0.7710 (t70) cc_final: 0.7476 (t0) REVERT: A 227 GLU cc_start: 0.7997 (tt0) cc_final: 0.7669 (tt0) REVERT: B 128 ARG cc_start: 0.7492 (mmt180) cc_final: 0.6997 (mmt180) REVERT: C 128 ARG cc_start: 0.7569 (mmt180) cc_final: 0.7224 (mmt180) REVERT: C 181 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8144 (mm-30) REVERT: D 128 ARG cc_start: 0.7434 (mmt180) cc_final: 0.7018 (mmt180) REVERT: E 128 ARG cc_start: 0.7631 (mmt180) cc_final: 0.7301 (mmt180) REVERT: E 187 GLU cc_start: 0.8132 (tt0) cc_final: 0.7845 (tt0) REVERT: E 221 MET cc_start: 0.8514 (mtm) cc_final: 0.8223 (mtm) REVERT: F 128 ARG cc_start: 0.7386 (mmt180) cc_final: 0.6983 (mmt180) REVERT: G 187 GLU cc_start: 0.8147 (tt0) cc_final: 0.7888 (tt0) outliers start: 11 outliers final: 10 residues processed: 166 average time/residue: 0.3099 time to fit residues: 76.4249 Evaluate side-chains 161 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 171 ILE 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 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 114 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.142439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.114814 restraints weight = 16919.074| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.67 r_work: 0.3048 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 16233 Z= 0.159 Angle : 0.594 7.533 21847 Z= 0.255 Chirality : 0.047 0.397 2856 Planarity : 0.003 0.053 2450 Dihedral : 14.559 112.736 5278 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.67 % Allowed : 9.84 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.19), residues: 1820 helix: 3.38 (0.14), residues: 1036 sheet: 0.00 (0.27), residues: 308 loop : -1.12 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 240 PHE 0.009 0.001 PHE B 188 TYR 0.004 0.001 TYR C 27 ARG 0.010 0.000 ARG E 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2765.06 seconds wall clock time: 52 minutes 16.44 seconds (3136.44 seconds total)