Starting phenix.real_space_refine on Wed Mar 4 20:43:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oo0_13003/03_2026/7oo0_13003.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oo0_13003/03_2026/7oo0_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 { model { file = "/net/cci-nas-00/data/ceres_data/7oo0_13003/03_2026/7oo0_13003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oo0_13003/03_2026/7oo0_13003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oo0_13003/03_2026/7oo0_13003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oo0_13003/03_2026/7oo0_13003.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.46, per 1000 atoms: 0.22 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: 1.51 Conformation dependent library (CDL) restraints added in 690.2 milliseconds 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: 0.40 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: 2.51 Time building geometry restraints manager: 1.98 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: 1.120 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 14.360 Find NCS groups from input model: 0.400 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: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.320 ------------------------------------------------------------------------------- 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 are 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 : 0.498 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: 0.7636 (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: 0.7561 (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: 0.8755 (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: 0.1544 time to fit residues: 29.8681 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 : 0.500 ------------------------------------------------------------------------------- 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 are 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 : 0.519 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: 0.1393 time to fit residues: 29.6514 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 : 0.522 ------------------------------------------------------------------------------- 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 are 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 : 0.459 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: 0.1360 time to fit residues: 30.0769 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 : 0.479 ------------------------------------------------------------------------------- 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 are 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 : 0.518 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: 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: 0.8185 (mtm) REVERT: E 128 ARG cc_start: 0.7934 (mmt180) cc_final: 0.7401 (mmt180) REVERT: E 221 MET cc_start: 0.8803 (mtm) cc_final: 0.8477 (mtm) REVERT: F 128 ARG cc_start: 0.7636 (mmt180) cc_final: 0.7201 (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: 0.1420 time to fit residues: 33.0494 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 : 0.486 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.139850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.111926 restraints weight = 17015.433| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.75 r_work: 0.3012 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1931 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= 0.121 Angle : 0.639 7.587 21847 Z= 0.269 Chirality : 0.050 0.359 2856 Planarity : 0.003 0.051 2450 Dihedral : 16.853 120.507 5278 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.01 % Allowed : 8.56 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.19), residues: 1820 helix: 3.03 (0.15), residues: 1036 sheet: -0.42 (0.27), residues: 308 loop : -1.06 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 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 0.00272 (16233) covalent geometry : angle 0.63862 (21847) hydrogen bonds : bond 0.03582 ( 994) hydrogen bonds : angle 3.68091 ( 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 164 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.478 Fit side-chains REVERT: A 128 ARG cc_start: 0.7745 (mmt180) cc_final: 0.7331 (mmt180) REVERT: A 227 GLU cc_start: 0.8554 (tt0) cc_final: 0.8278 (tt0) REVERT: B 58 SER cc_start: 0.7199 (t) cc_final: 0.6983 (t) REVERT: B 128 ARG cc_start: 0.7711 (mmt180) cc_final: 0.7229 (mmt180) REVERT: C 128 ARG cc_start: 0.7884 (mmt180) cc_final: 0.7573 (mmt180) REVERT: D 128 ARG cc_start: 0.7621 (mmt180) cc_final: 0.7267 (mmt180) REVERT: D 221 MET cc_start: 0.8391 (mtm) cc_final: 0.8186 (mtm) REVERT: E 128 ARG cc_start: 0.7909 (mmt180) cc_final: 0.7389 (mmt180) REVERT: E 221 MET cc_start: 0.8764 (mtm) cc_final: 0.8443 (mtm) REVERT: F 128 ARG cc_start: 0.7596 (mmt180) cc_final: 0.7184 (mmt180) REVERT: G 187 GLU cc_start: 0.8691 (tt0) cc_final: 0.8484 (tt0) outliers start: 15 outliers final: 10 residues processed: 161 average time/residue: 0.1403 time to fit residues: 33.0163 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 : 0.522 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 149 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 167 optimal weight: 0.0970 chunk 120 optimal weight: 0.0770 chunk 124 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 overall best weight: 0.5936 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.142625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.115074 restraints weight = 16900.596| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.68 r_work: 0.3049 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16233 Z= 0.104 Angle : 0.589 6.579 21847 Z= 0.251 Chirality : 0.047 0.320 2856 Planarity : 0.003 0.055 2450 Dihedral : 16.033 119.462 5278 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.81 % Allowed : 8.89 % 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 are not related in a simple way. whole: 2.46 (0.19), residues: 1820 helix: 3.33 (0.14), residues: 1036 sheet: -0.30 (0.27), residues: 308 loop : -1.02 (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 C 75 PHE 0.007 0.001 PHE F 188 TRP 0.002 0.000 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00220 (16233) covalent geometry : angle 0.58925 (21847) hydrogen bonds : bond 0.03301 ( 994) hydrogen bonds : angle 3.53746 ( 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 170 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.575 Fit side-chains REVERT: A 128 ARG cc_start: 0.7814 (mmt180) cc_final: 0.7385 (mmt180) REVERT: A 137 ASP cc_start: 0.8264 (t70) cc_final: 0.8002 (t0) REVERT: A 227 GLU cc_start: 0.8566 (tt0) cc_final: 0.8299 (tt0) REVERT: B 128 ARG cc_start: 0.7812 (mmt180) cc_final: 0.7347 (mmt180) REVERT: C 128 ARG cc_start: 0.7829 (mmt180) cc_final: 0.7509 (mmt180) REVERT: D 59 ARG cc_start: 0.6861 (mtt-85) cc_final: 0.6659 (mtt-85) REVERT: D 128 ARG cc_start: 0.7669 (mmt180) cc_final: 0.7304 (mmt180) REVERT: E 128 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7414 (mmt180) REVERT: E 221 MET cc_start: 0.8747 (mtm) cc_final: 0.8441 (mtm) REVERT: F 128 ARG cc_start: 0.7640 (mmt180) cc_final: 0.7216 (mmt180) REVERT: F 149 GLN cc_start: 0.8344 (mt0) cc_final: 0.8136 (mt0) REVERT: G 187 GLU cc_start: 0.8738 (tt0) cc_final: 0.8527 (tt0) outliers start: 12 outliers final: 6 residues processed: 167 average time/residue: 0.1329 time to fit residues: 32.5230 Evaluate side-chains 155 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 106 optimal weight: 4.9990 chunk 160 optimal weight: 0.0970 chunk 153 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.0570 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.142472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.114939 restraints weight = 16866.122| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.67 r_work: 0.3050 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16233 Z= 0.105 Angle : 0.588 6.860 21847 Z= 0.251 Chirality : 0.047 0.323 2856 Planarity : 0.003 0.053 2450 Dihedral : 15.697 118.358 5278 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.28 % Allowed : 8.96 % 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 are not related in a simple way. whole: 2.53 (0.19), residues: 1820 helix: 3.38 (0.14), residues: 1036 sheet: -0.23 (0.26), 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 F 75 PHE 0.008 0.001 PHE F 188 TRP 0.002 0.000 TRP A 240 Details of bonding type rmsd covalent geometry : bond 0.00227 (16233) covalent geometry : angle 0.58766 (21847) hydrogen bonds : bond 0.03317 ( 994) hydrogen bonds : angle 3.53972 ( 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: 19 poor density : 151 time to evaluate : 0.542 Fit side-chains REVERT: A 24 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6799 (mp) REVERT: A 128 ARG cc_start: 0.7838 (mmt180) cc_final: 0.7428 (mmt180) REVERT: A 137 ASP cc_start: 0.8266 (t70) cc_final: 0.7998 (t0) REVERT: A 155 MET cc_start: 0.8796 (ptp) cc_final: 0.8336 (ptp) REVERT: A 227 GLU cc_start: 0.8562 (tt0) cc_final: 0.8294 (tt0) REVERT: B 24 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6714 (mp) REVERT: B 128 ARG cc_start: 0.7780 (mmt180) cc_final: 0.7315 (mmt180) REVERT: C 24 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6880 (mp) REVERT: C 128 ARG cc_start: 0.7889 (mmt180) cc_final: 0.7595 (mmt180) REVERT: D 24 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6695 (mp) REVERT: D 128 ARG cc_start: 0.7685 (mmt180) cc_final: 0.7303 (mmt180) REVERT: E 128 ARG cc_start: 0.7912 (mmt180) cc_final: 0.7464 (mmt180) REVERT: E 221 MET cc_start: 0.8758 (mtm) cc_final: 0.8460 (mtm) REVERT: F 24 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6841 (mp) REVERT: F 31 ILE cc_start: 0.7210 (mt) cc_final: 0.6998 (mp) REVERT: F 128 ARG cc_start: 0.7640 (mmt180) cc_final: 0.7218 (mmt180) REVERT: G 187 GLU cc_start: 0.8758 (tt0) cc_final: 0.8553 (tt0) outliers start: 19 outliers final: 11 residues processed: 168 average time/residue: 0.1299 time to fit residues: 32.4787 Evaluate side-chains 163 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 58 SER 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 171 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 24 LEU 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: 4.9990 chunk 35 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 133 optimal weight: 0.5980 chunk 159 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.140778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.113089 restraints weight = 17072.278| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.68 r_work: 0.3025 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16233 Z= 0.132 Angle : 0.612 7.517 21847 Z= 0.262 Chirality : 0.048 0.368 2856 Planarity : 0.003 0.057 2450 Dihedral : 15.504 116.590 5278 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.35 % Allowed : 8.96 % 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 are not related in a simple way. whole: 2.41 (0.19), residues: 1820 helix: 3.24 (0.14), residues: 1036 sheet: -0.15 (0.26), residues: 308 loop : -1.07 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 59 TYR 0.005 0.001 TYR C 75 PHE 0.010 0.001 PHE G 188 TRP 0.003 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00307 (16233) covalent geometry : angle 0.61209 (21847) hydrogen bonds : bond 0.03534 ( 994) hydrogen bonds : angle 3.62715 ( 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 170 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.498 Fit side-chains REVERT: A 24 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6879 (mp) REVERT: A 128 ARG cc_start: 0.7842 (mmt180) cc_final: 0.7405 (mmt180) REVERT: A 137 ASP cc_start: 0.8275 (t70) cc_final: 0.7984 (t0) REVERT: A 155 MET cc_start: 0.8839 (ptp) cc_final: 0.8460 (ptp) REVERT: A 227 GLU cc_start: 0.8560 (tt0) cc_final: 0.8290 (tt0) REVERT: B 24 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6710 (mp) REVERT: B 128 ARG cc_start: 0.7784 (mmt180) cc_final: 0.7325 (mmt180) REVERT: C 24 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6880 (mp) REVERT: C 128 ARG cc_start: 0.7805 (mmt180) cc_final: 0.7480 (mmt180) REVERT: D 24 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6695 (mp) REVERT: D 128 ARG cc_start: 0.7684 (mmt180) cc_final: 0.7347 (mmt180) REVERT: E 128 ARG cc_start: 0.7877 (mmt180) cc_final: 0.7402 (mmt180) REVERT: E 221 MET cc_start: 0.8797 (mtm) cc_final: 0.8491 (mtm) REVERT: F 24 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6834 (mp) REVERT: F 128 ARG cc_start: 0.7618 (mmt180) cc_final: 0.7206 (mmt180) REVERT: G 187 GLU cc_start: 0.8755 (tt0) cc_final: 0.8547 (tt0) outliers start: 20 outliers final: 10 residues processed: 168 average time/residue: 0.1338 time to fit residues: 33.4826 Evaluate side-chains 163 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 24 LEU 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 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 24 LEU 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: 2.9990 chunk 71 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 63 optimal weight: 0.0030 chunk 159 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.142483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.114821 restraints weight = 16941.659| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.67 r_work: 0.3047 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16233 Z= 0.107 Angle : 0.588 7.052 21847 Z= 0.252 Chirality : 0.047 0.380 2856 Planarity : 0.003 0.056 2450 Dihedral : 15.073 115.021 5278 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 1.21 % Allowed : 8.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.19), residues: 1820 helix: 3.39 (0.14), residues: 1036 sheet: -0.08 (0.27), residues: 308 loop : -1.05 (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 C 75 PHE 0.009 0.001 PHE F 188 TRP 0.002 0.000 TRP A 240 Details of bonding type rmsd covalent geometry : bond 0.00235 (16233) covalent geometry : angle 0.58795 (21847) hydrogen bonds : bond 0.03307 ( 994) hydrogen bonds : angle 3.52855 ( 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 : 0.504 Fit side-chains REVERT: A 24 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6788 (mp) REVERT: A 128 ARG cc_start: 0.7880 (mmt180) cc_final: 0.7453 (mmt180) REVERT: A 137 ASP cc_start: 0.8273 (t70) cc_final: 0.7994 (t0) REVERT: A 155 MET cc_start: 0.8827 (ptp) cc_final: 0.8463 (ptp) REVERT: A 227 GLU cc_start: 0.8560 (tt0) cc_final: 0.8290 (tt0) REVERT: B 24 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6686 (mp) REVERT: B 128 ARG cc_start: 0.7790 (mmt180) cc_final: 0.7334 (mmt180) REVERT: C 24 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6871 (mp) REVERT: C 128 ARG cc_start: 0.7821 (mmt180) cc_final: 0.7499 (mmt180) REVERT: D 24 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6638 (mp) REVERT: D 128 ARG cc_start: 0.7780 (mmt180) cc_final: 0.7435 (mmt180) REVERT: E 128 ARG cc_start: 0.7878 (mmt180) cc_final: 0.7425 (mmt180) REVERT: E 221 MET cc_start: 0.8747 (mtm) cc_final: 0.8463 (mtm) REVERT: F 24 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6825 (mp) REVERT: F 128 ARG cc_start: 0.7630 (mmt180) cc_final: 0.7228 (mmt180) REVERT: G 187 GLU cc_start: 0.8776 (tt0) cc_final: 0.8575 (tt0) outliers start: 18 outliers final: 11 residues processed: 164 average time/residue: 0.1282 time to fit residues: 31.3238 Evaluate side-chains 163 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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 171 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 30 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 70 optimal weight: 0.9990 chunk 155 optimal weight: 0.0270 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 59 optimal weight: 0.0980 chunk 99 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.3640 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.146443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.118815 restraints weight = 16709.418| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.68 r_work: 0.3103 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2605 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= 0.093 Angle : 0.557 7.435 21847 Z= 0.239 Chirality : 0.046 0.393 2856 Planarity : 0.003 0.053 2450 Dihedral : 13.891 112.124 5278 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.81 % Allowed : 9.50 % 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 are not related in a simple way. whole: 2.76 (0.19), residues: 1820 helix: 3.62 (0.15), residues: 1043 sheet: -0.22 (0.27), residues: 294 loop : -1.07 (0.23), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 59 TYR 0.004 0.001 TYR D 135 PHE 0.008 0.001 PHE D 188 TRP 0.002 0.000 TRP C 251 Details of bonding type rmsd covalent geometry : bond 0.00190 (16233) covalent geometry : angle 0.55659 (21847) hydrogen bonds : bond 0.02993 ( 994) hydrogen bonds : angle 3.34694 ( 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 174 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.531 Fit side-chains REVERT: A 128 ARG cc_start: 0.7905 (mmt180) cc_final: 0.7472 (mmt180) REVERT: A 155 MET cc_start: 0.8774 (ptp) cc_final: 0.8459 (ptp) REVERT: A 227 GLU cc_start: 0.8486 (tt0) cc_final: 0.8183 (tt0) REVERT: B 24 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6626 (mp) REVERT: B 128 ARG cc_start: 0.7739 (mmt180) cc_final: 0.7324 (mmt180) REVERT: B 149 GLN cc_start: 0.8313 (mt0) cc_final: 0.7699 (mm-40) REVERT: C 128 ARG cc_start: 0.7846 (mmt180) cc_final: 0.7533 (mmt180) REVERT: D 24 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6706 (mp) REVERT: D 128 ARG cc_start: 0.7715 (mmt180) cc_final: 0.7351 (mmt180) REVERT: E 128 ARG cc_start: 0.7960 (mmt180) cc_final: 0.7473 (mmt180) REVERT: E 221 MET cc_start: 0.8666 (mtm) cc_final: 0.8403 (mtm) REVERT: F 128 ARG cc_start: 0.7626 (mmt180) cc_final: 0.7219 (mmt180) REVERT: G 149 GLN cc_start: 0.8285 (mt0) cc_final: 0.7696 (mm-40) outliers start: 12 outliers final: 4 residues processed: 171 average time/residue: 0.1338 time to fit residues: 34.0051 Evaluate side-chains 162 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 125 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 169 optimal weight: 0.0070 chunk 49 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.140439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.112579 restraints weight = 16933.202| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.68 r_work: 0.3018 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2382 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= 0.154 Angle : 0.626 7.328 21847 Z= 0.272 Chirality : 0.047 0.383 2856 Planarity : 0.003 0.059 2450 Dihedral : 13.574 109.107 5278 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.19), residues: 1820 helix: 3.20 (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 ARG 0.011 0.001 ARG C 88 TYR 0.006 0.001 TYR B 250 PHE 0.010 0.001 PHE G 188 TRP 0.003 0.001 TRP A 240 Details of bonding type rmsd covalent geometry : bond 0.00363 (16233) covalent geometry : angle 0.62551 (21847) hydrogen bonds : bond 0.03668 ( 994) hydrogen bonds : angle 3.65204 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3432.72 seconds wall clock time: 59 minutes 44.67 seconds (3584.67 seconds total)