Starting phenix.real_space_refine on Wed Feb 4 23:35:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lag_62927/02_2026/9lag_62927.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lag_62927/02_2026/9lag_62927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lag_62927/02_2026/9lag_62927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lag_62927/02_2026/9lag_62927.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lag_62927/02_2026/9lag_62927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lag_62927/02_2026/9lag_62927.map" } resolution = 2.96 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= 0.001 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 25 5.49 5 S 20 5.16 5 C 8990 2.51 5 N 2030 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13535 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "E" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "C" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "D" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "A" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 202 Unusual residues: {'PEE': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 154 Unusual residues: {'PEE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 178 Unusual residues: {'PEE': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 178 Unusual residues: {'PEE': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 178 Unusual residues: {'PEE': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.28, per 1000 atoms: 0.24 Number of scatterers: 13535 At special positions: 0 Unit cell: (98.8, 98.04, 119.32, 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 20 16.00 P 25 15.00 O 2470 8.00 N 2030 7.00 C 8990 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: 1.11 Conformation dependent library (CDL) restraints added in 620.4 milliseconds 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 37.8% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 196 through 214 removed outlier: 4.969A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 215 through 218 removed outlier: 3.593A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 218' Processing helix chain 'A' and resid 220 through 243 Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.854A pdb=" N ARG A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'E' and resid 57 through 61 Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 196 through 214 removed outlier: 4.969A pdb=" N LEU E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) Proline residue: E 204 - end of helix Processing helix chain 'E' and resid 215 through 218 removed outlier: 3.593A pdb=" N SER E 218 " --> pdb=" O ALA E 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 220 through 243 Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 315 removed outlier: 3.854A pdb=" N ARG E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 196 through 214 removed outlier: 4.969A pdb=" N LEU B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 215 through 218 removed outlier: 3.593A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 215 through 218' Processing helix chain 'B' and resid 220 through 243 Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.855A pdb=" N ARG B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 196 through 214 removed outlier: 4.969A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Proline residue: C 204 - end of helix Processing helix chain 'C' and resid 215 through 218 removed outlier: 3.594A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 218' Processing helix chain 'C' and resid 220 through 243 Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.854A pdb=" N ARG C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 196 through 214 removed outlier: 4.969A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Proline residue: D 204 - end of helix Processing helix chain 'D' and resid 215 through 218 removed outlier: 3.593A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 215 through 218' Processing helix chain 'D' and resid 220 through 243 Processing helix chain 'D' and resid 253 through 282 Processing helix chain 'D' and resid 284 through 315 removed outlier: 3.853A pdb=" N ARG D 296 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 7.175A pdb=" N LEU A 103 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE A 92 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN A 101 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 100 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP A 47 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 16 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA A 143 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL A 18 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 removed outlier: 7.175A pdb=" N LEU A 103 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE A 92 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN A 101 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 100 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP A 47 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR A 36 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER A 29 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LYS A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N CYS A 27 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A 40 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 23 " --> pdb=" O PHE A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 7.162A pdb=" N LYS A 183 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL A 169 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 64 through 65 removed outlier: 7.176A pdb=" N LEU E 103 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE E 92 " --> pdb=" O GLN E 101 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN E 101 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL E 100 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP E 47 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 7.176A pdb=" N LEU E 103 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE E 92 " --> pdb=" O GLN E 101 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN E 101 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL E 100 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP E 47 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR E 36 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER E 29 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR E 23 " --> pdb=" O PHE E 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 76 through 78 removed outlier: 7.161A pdb=" N LYS E 183 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL E 169 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 65 removed outlier: 7.175A pdb=" N LEU B 103 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE B 92 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN B 101 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 100 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP B 47 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 65 removed outlier: 7.175A pdb=" N LEU B 103 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE B 92 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN B 101 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 100 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP B 47 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR B 36 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER B 29 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 23 " --> pdb=" O PHE B 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 76 through 78 removed outlier: 7.162A pdb=" N LYS B 183 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL B 169 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 64 through 65 removed outlier: 7.176A pdb=" N LEU C 103 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE C 92 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN C 101 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL C 100 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 64 through 65 removed outlier: 7.176A pdb=" N LEU C 103 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE C 92 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN C 101 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL C 100 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR C 36 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER C 29 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 23 " --> pdb=" O PHE C 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 7.162A pdb=" N LYS C 183 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL C 169 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 64 through 65 removed outlier: 7.175A pdb=" N LEU D 103 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE D 92 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN D 101 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 100 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP D 47 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 64 through 65 removed outlier: 7.175A pdb=" N LEU D 103 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE D 92 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN D 101 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 100 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP D 47 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR D 36 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER D 29 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LYS D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N CYS D 27 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN D 40 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR D 23 " --> pdb=" O PHE D 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 7.162A pdb=" N LYS D 183 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL D 169 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1890 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: 1.98 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2196 1.33 - 1.45: 3639 1.45 - 1.57: 7925 1.57 - 1.69: 50 1.69 - 1.81: 35 Bond restraints: 13845 Sorted by residual: bond pdb=" N LEU E 114 " pdb=" CA LEU E 114 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.21e-02 6.83e+03 8.78e+00 bond pdb=" N LEU A 114 " pdb=" CA LEU A 114 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.21e-02 6.83e+03 8.46e+00 bond pdb=" N LEU B 114 " pdb=" CA LEU B 114 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.33e+00 bond pdb=" N LEU D 114 " pdb=" CA LEU D 114 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.30e+00 bond pdb=" N LEU C 114 " pdb=" CA LEU C 114 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.20e+00 ... (remaining 13840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 18256 1.24 - 2.48: 308 2.48 - 3.71: 117 3.71 - 4.95: 39 4.95 - 6.19: 10 Bond angle restraints: 18730 Sorted by residual: angle pdb=" N ARG D 117 " pdb=" CA ARG D 117 " pdb=" C ARG D 117 " ideal model delta sigma weight residual 110.53 104.34 6.19 1.32e+00 5.74e-01 2.20e+01 angle pdb=" N ARG C 117 " pdb=" CA ARG C 117 " pdb=" C ARG C 117 " ideal model delta sigma weight residual 110.53 104.34 6.19 1.32e+00 5.74e-01 2.20e+01 angle pdb=" N ARG E 117 " pdb=" CA ARG E 117 " pdb=" C ARG E 117 " ideal model delta sigma weight residual 110.53 104.35 6.18 1.32e+00 5.74e-01 2.20e+01 angle pdb=" N ARG A 117 " pdb=" CA ARG A 117 " pdb=" C ARG A 117 " ideal model delta sigma weight residual 110.53 104.36 6.17 1.32e+00 5.74e-01 2.19e+01 angle pdb=" N ARG B 117 " pdb=" CA ARG B 117 " pdb=" C ARG B 117 " ideal model delta sigma weight residual 110.53 104.38 6.15 1.32e+00 5.74e-01 2.17e+01 ... (remaining 18725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.54: 8160 31.54 - 63.08: 185 63.08 - 94.63: 15 94.63 - 126.17: 30 126.17 - 157.71: 15 Dihedral angle restraints: 8405 sinusoidal: 3725 harmonic: 4680 Sorted by residual: dihedral pdb=" C4 PEE C 406 " pdb=" O4P PEE C 406 " pdb=" P PEE C 406 " pdb=" O2P PEE C 406 " ideal model delta sinusoidal sigma weight residual -75.78 81.93 -157.71 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C4 PEE B 406 " pdb=" O4P PEE B 406 " pdb=" P PEE B 406 " pdb=" O2P PEE B 406 " ideal model delta sinusoidal sigma weight residual -75.78 81.91 -157.69 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C4 PEE A 405 " pdb=" O4P PEE A 405 " pdb=" P PEE A 405 " pdb=" O2P PEE A 405 " ideal model delta sinusoidal sigma weight residual -75.78 81.90 -157.68 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 8402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1473 0.036 - 0.073: 381 0.073 - 0.109: 198 0.109 - 0.146: 38 0.146 - 0.182: 10 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CA ARG C 117 " pdb=" N ARG C 117 " pdb=" C ARG C 117 " pdb=" CB ARG C 117 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA ARG A 117 " pdb=" N ARG A 117 " pdb=" C ARG A 117 " pdb=" CB ARG A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CA ARG D 117 " pdb=" N ARG D 117 " pdb=" C ARG D 117 " pdb=" CB ARG D 117 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 2097 not shown) Planarity restraints: 2275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 117 " -0.158 9.50e-02 1.11e+02 7.08e-02 3.09e+00 pdb=" NE ARG E 117 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG E 117 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG E 117 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 117 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 117 " 0.158 9.50e-02 1.11e+02 7.07e-02 3.07e+00 pdb=" NE ARG C 117 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG C 117 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 117 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 117 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 117 " 0.157 9.50e-02 1.11e+02 7.06e-02 3.06e+00 pdb=" NE ARG D 117 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG D 117 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 117 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 117 " 0.006 2.00e-02 2.50e+03 ... (remaining 2272 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3294 2.81 - 3.33: 12062 3.33 - 3.85: 20646 3.85 - 4.38: 23889 4.38 - 4.90: 42445 Nonbonded interactions: 102336 Sorted by model distance: nonbonded pdb=" O ILE C 211 " pdb=" OG1 THR C 214 " model vdw 2.285 3.040 nonbonded pdb=" O ILE B 211 " pdb=" OG1 THR B 214 " model vdw 2.285 3.040 nonbonded pdb=" O ILE E 211 " pdb=" OG1 THR E 214 " model vdw 2.285 3.040 nonbonded pdb=" O ILE A 211 " pdb=" OG1 THR A 214 " model vdw 2.285 3.040 nonbonded pdb=" O ILE D 211 " pdb=" OG1 THR D 214 " model vdw 2.285 3.040 ... (remaining 102331 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 5 through 401 or (resid 402 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name O1P or name O2 or name O2P \ or name O3 or name O3P or name O4 or name O4P or name O5 or name P )))) selection = (chain 'B' and (resid 5 through 316 or (resid 401 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P \ or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 \ or name P )) or (resid 402 and (name C1 or name C10 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C2 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name O1P or name O2 or name O2P or name O3 or name O3P \ or name O4 or name O4P or name O5 or name P )))) selection = (chain 'C' and (resid 5 through 316 or (resid 401 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P \ or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 \ or name P )) or (resid 402 and (name C1 or name C10 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C2 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name O1P or name O2 or name O2P or name O3 or name O3P \ or name O4 or name O4P or name O5 or name P )))) selection = (chain 'D' and (resid 5 through 316 or (resid 401 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P \ or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 \ or name P )) or (resid 402 and (name C1 or name C10 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C2 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name O1P or name O2 or name O2P or name O3 or name O3P \ or name O4 or name O4P or name O5 or name P )))) selection = (chain 'E' and (resid 5 through 316 or (resid 401 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P \ or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 \ or name P )) or (resid 402 and (name C1 or name C10 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C2 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name O1P or name O2 or name O2P or name O3 or name O3P \ or name O4 or name O4P or name O5 or name P )))) } 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: 1.780 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.450 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13845 Z= 0.162 Angle : 0.512 6.189 18730 Z= 0.306 Chirality : 0.043 0.182 2100 Planarity : 0.005 0.071 2275 Dihedral : 16.656 157.710 5355 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.36 % Allowed : 4.43 % Favored : 95.21 % 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: 0.90 (0.22), residues: 1550 helix: 3.20 (0.21), residues: 515 sheet: -0.23 (0.27), residues: 370 loop : -1.06 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 117 TYR 0.009 0.001 TYR D 254 PHE 0.007 0.001 PHE D 116 TRP 0.002 0.000 TRP E 160 HIS 0.003 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00241 (13845) covalent geometry : angle 0.51193 (18730) hydrogen bonds : bond 0.15949 ( 590) hydrogen bonds : angle 6.42171 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 272 time to evaluate : 0.521 Fit side-chains REVERT: A 83 ASN cc_start: 0.8133 (p0) cc_final: 0.7874 (m110) REVERT: A 88 ASP cc_start: 0.7104 (m-30) cc_final: 0.6751 (m-30) REVERT: E 88 ASP cc_start: 0.6590 (m-30) cc_final: 0.6282 (m-30) REVERT: E 102 TYR cc_start: 0.8294 (t80) cc_final: 0.7761 (t80) REVERT: E 161 ASP cc_start: 0.7242 (p0) cc_final: 0.6952 (p0) REVERT: B 102 TYR cc_start: 0.8178 (t80) cc_final: 0.7730 (t80) REVERT: B 161 ASP cc_start: 0.7078 (p0) cc_final: 0.6862 (p0) REVERT: C 102 TYR cc_start: 0.8224 (t80) cc_final: 0.7877 (t80) REVERT: C 161 ASP cc_start: 0.7060 (p0) cc_final: 0.6782 (p0) REVERT: D 101 GLN cc_start: 0.7501 (mm-40) cc_final: 0.6931 (mm-40) REVERT: D 102 TYR cc_start: 0.8162 (t80) cc_final: 0.7555 (t80) REVERT: D 145 ASP cc_start: 0.6842 (p0) cc_final: 0.6585 (p0) REVERT: D 161 ASP cc_start: 0.7111 (p0) cc_final: 0.6904 (p0) REVERT: D 187 GLN cc_start: 0.8602 (mt0) cc_final: 0.8400 (mt0) outliers start: 5 outliers final: 7 residues processed: 277 average time/residue: 0.5355 time to fit residues: 163.8084 Evaluate side-chains 214 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 207 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 94 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN E 101 GLN B 101 GLN B 124 GLN C 101 GLN D 40 ASN D 101 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.180266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105407 restraints weight = 14596.107| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.35 r_work: 0.2898 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13845 Z= 0.195 Angle : 0.575 5.855 18730 Z= 0.299 Chirality : 0.045 0.138 2100 Planarity : 0.004 0.044 2275 Dihedral : 19.839 122.491 2439 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.21 % Allowed : 8.86 % Favored : 86.93 % 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: 0.74 (0.21), residues: 1550 helix: 2.82 (0.21), residues: 520 sheet: -0.15 (0.25), residues: 375 loop : -1.07 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 189 TYR 0.014 0.002 TYR A 102 PHE 0.013 0.001 PHE A 216 TRP 0.009 0.002 TRP B 213 HIS 0.004 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00455 (13845) covalent geometry : angle 0.57497 (18730) hydrogen bonds : bond 0.07640 ( 590) hydrogen bonds : angle 5.19767 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 0.630 Fit side-chains REVERT: A 44 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7594 (p) REVERT: A 77 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8026 (mmp80) REVERT: A 88 ASP cc_start: 0.6740 (m-30) cc_final: 0.6138 (m-30) REVERT: A 101 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7101 (mm-40) REVERT: A 122 ASP cc_start: 0.8641 (p0) cc_final: 0.8352 (p0) REVERT: A 161 ASP cc_start: 0.6964 (p0) cc_final: 0.6734 (p0) REVERT: A 189 ARG cc_start: 0.7813 (mtp-110) cc_final: 0.7451 (mtp85) REVERT: A 272 GLU cc_start: 0.9280 (tm-30) cc_final: 0.8722 (tm-30) REVERT: E 44 SER cc_start: 0.8285 (OUTLIER) cc_final: 0.7795 (p) REVERT: E 77 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7961 (mmp80) REVERT: E 102 TYR cc_start: 0.7779 (t80) cc_final: 0.7272 (t80) REVERT: E 161 ASP cc_start: 0.7274 (p0) cc_final: 0.7009 (p0) REVERT: E 272 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8423 (tm-30) REVERT: B 44 SER cc_start: 0.8414 (t) cc_final: 0.8110 (p) REVERT: B 101 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6960 (mm-40) REVERT: B 102 TYR cc_start: 0.7672 (t80) cc_final: 0.7357 (t80) REVERT: B 122 ASP cc_start: 0.8865 (p0) cc_final: 0.8601 (p0) REVERT: B 161 ASP cc_start: 0.7171 (p0) cc_final: 0.6947 (p0) REVERT: B 272 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8659 (tm-30) REVERT: C 44 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.7781 (p) REVERT: C 77 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7876 (mmp80) REVERT: C 102 TYR cc_start: 0.7736 (t80) cc_final: 0.7442 (t80) REVERT: C 161 ASP cc_start: 0.7271 (p0) cc_final: 0.6983 (p0) REVERT: C 272 GLU cc_start: 0.9257 (tm-30) cc_final: 0.8596 (tm-30) REVERT: D 44 SER cc_start: 0.8376 (t) cc_final: 0.8159 (p) REVERT: D 75 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7677 (mm-30) REVERT: D 101 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6828 (mm-40) REVERT: D 161 ASP cc_start: 0.7326 (p0) cc_final: 0.7097 (p0) REVERT: D 205 MET cc_start: 0.8298 (mmt) cc_final: 0.8085 (mmt) REVERT: D 252 MET cc_start: 0.8531 (mmm) cc_final: 0.8252 (mmp) REVERT: D 272 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8618 (tm-30) outliers start: 59 outliers final: 23 residues processed: 269 average time/residue: 0.5596 time to fit residues: 164.8273 Evaluate side-chains 258 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 149 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 2 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN E 101 GLN B 40 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN C 101 GLN D 40 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.181685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106702 restraints weight = 14584.066| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.29 r_work: 0.2902 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13845 Z= 0.156 Angle : 0.537 5.756 18730 Z= 0.279 Chirality : 0.044 0.131 2100 Planarity : 0.004 0.042 2275 Dihedral : 18.445 102.606 2434 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.86 % Allowed : 11.21 % Favored : 84.93 % 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: 0.85 (0.21), residues: 1550 helix: 2.88 (0.21), residues: 515 sheet: -0.09 (0.25), residues: 375 loop : -0.94 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 109 TYR 0.009 0.001 TYR A 102 PHE 0.012 0.001 PHE B 37 TRP 0.007 0.001 TRP D 47 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00364 (13845) covalent geometry : angle 0.53674 (18730) hydrogen bonds : bond 0.07015 ( 590) hydrogen bonds : angle 4.83125 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 0.500 Fit side-chains REVERT: A 38 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7693 (mtpt) REVERT: A 44 SER cc_start: 0.8151 (OUTLIER) cc_final: 0.7687 (p) REVERT: A 77 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7883 (mmp80) REVERT: A 88 ASP cc_start: 0.6687 (m-30) cc_final: 0.6185 (m-30) REVERT: A 91 ASP cc_start: 0.7704 (p0) cc_final: 0.7272 (t0) REVERT: A 189 ARG cc_start: 0.7880 (mtp-110) cc_final: 0.7528 (mtp85) REVERT: A 272 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8596 (tm-30) REVERT: E 44 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.7788 (p) REVERT: E 76 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8469 (mp) REVERT: E 88 ASP cc_start: 0.7081 (m-30) cc_final: 0.6449 (OUTLIER) REVERT: E 102 TYR cc_start: 0.7818 (t80) cc_final: 0.7359 (t80) REVERT: E 161 ASP cc_start: 0.7297 (p0) cc_final: 0.7067 (p0) REVERT: E 272 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8608 (tm-30) REVERT: B 44 SER cc_start: 0.8397 (t) cc_final: 0.8180 (p) REVERT: B 76 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8467 (mp) REVERT: B 272 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8587 (tm-30) REVERT: C 44 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7810 (p) REVERT: C 76 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8435 (mp) REVERT: C 77 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7943 (mmp80) REVERT: C 161 ASP cc_start: 0.7326 (p0) cc_final: 0.7086 (p0) REVERT: C 272 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8553 (tm-30) REVERT: D 101 GLN cc_start: 0.6884 (mm-40) cc_final: 0.6664 (mm-40) REVERT: D 272 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8590 (tm-30) outliers start: 54 outliers final: 34 residues processed: 249 average time/residue: 0.5492 time to fit residues: 150.4491 Evaluate side-chains 244 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 219 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 127 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 135 optimal weight: 0.0170 chunk 99 optimal weight: 5.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 40 ASN E 101 GLN B 40 ASN C 40 ASN C 101 GLN D 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.182007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106690 restraints weight = 14637.041| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.33 r_work: 0.2943 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13845 Z= 0.148 Angle : 0.529 5.762 18730 Z= 0.276 Chirality : 0.044 0.133 2100 Planarity : 0.004 0.045 2275 Dihedral : 16.830 100.277 2432 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.79 % Allowed : 11.50 % Favored : 83.71 % 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: 0.93 (0.21), residues: 1550 helix: 2.87 (0.21), residues: 515 sheet: -0.03 (0.25), residues: 375 loop : -0.83 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 109 TYR 0.008 0.001 TYR C 23 PHE 0.013 0.001 PHE D 37 TRP 0.008 0.001 TRP B 160 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00346 (13845) covalent geometry : angle 0.52876 (18730) hydrogen bonds : bond 0.06783 ( 590) hydrogen bonds : angle 4.61672 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 214 time to evaluate : 0.537 Fit side-chains REVERT: A 44 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7721 (p) REVERT: A 77 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8346 (mmt-90) REVERT: A 88 ASP cc_start: 0.6653 (m-30) cc_final: 0.6184 (m-30) REVERT: A 91 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7318 (t0) REVERT: A 161 ASP cc_start: 0.7126 (p0) cc_final: 0.6894 (p0) REVERT: A 189 ARG cc_start: 0.7843 (mtp-110) cc_final: 0.7477 (mtp85) REVERT: A 272 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8634 (tm-30) REVERT: E 44 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7739 (p) REVERT: E 76 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8500 (mp) REVERT: E 88 ASP cc_start: 0.7106 (m-30) cc_final: 0.6533 (OUTLIER) REVERT: B 76 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 272 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8571 (tm-30) REVERT: C 44 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.7792 (p) REVERT: C 161 ASP cc_start: 0.7300 (p0) cc_final: 0.7091 (p0) REVERT: C 272 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8586 (tm-30) REVERT: D 101 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6843 (mm-40) REVERT: D 161 ASP cc_start: 0.7182 (p0) cc_final: 0.6970 (p0) REVERT: D 272 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8559 (tm-30) outliers start: 67 outliers final: 45 residues processed: 240 average time/residue: 0.5692 time to fit residues: 149.9602 Evaluate side-chains 259 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 168 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 38 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 40 ASN E 101 GLN E 193 GLN B 40 ASN C 40 ASN C 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.181797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107465 restraints weight = 14712.127| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.33 r_work: 0.2965 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13845 Z= 0.122 Angle : 0.519 5.700 18730 Z= 0.269 Chirality : 0.043 0.131 2100 Planarity : 0.004 0.053 2275 Dihedral : 16.194 103.399 2432 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.71 % Allowed : 13.57 % Favored : 82.71 % 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: 1.09 (0.21), residues: 1550 helix: 3.00 (0.21), residues: 515 sheet: 0.07 (0.25), residues: 375 loop : -0.75 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 109 TYR 0.007 0.001 TYR C 254 PHE 0.012 0.001 PHE E 37 TRP 0.006 0.001 TRP B 160 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00268 (13845) covalent geometry : angle 0.51871 (18730) hydrogen bonds : bond 0.06032 ( 590) hydrogen bonds : angle 4.45868 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 0.478 Fit side-chains REVERT: A 44 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7733 (p) REVERT: A 77 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8356 (mmt-90) REVERT: A 91 ASP cc_start: 0.7640 (p0) cc_final: 0.7323 (t0) REVERT: A 161 ASP cc_start: 0.7097 (p0) cc_final: 0.6868 (p0) REVERT: A 189 ARG cc_start: 0.7861 (mtp-110) cc_final: 0.7507 (mtp85) REVERT: A 243 GLU cc_start: 0.8841 (tp30) cc_final: 0.8639 (tp30) REVERT: A 272 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8660 (tm-30) REVERT: E 44 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7786 (p) REVERT: E 76 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8537 (mp) REVERT: E 88 ASP cc_start: 0.7109 (m-30) cc_final: 0.6557 (OUTLIER) REVERT: B 161 ASP cc_start: 0.7022 (p0) cc_final: 0.6798 (p0) REVERT: B 272 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8471 (tm-30) REVERT: C 44 SER cc_start: 0.8304 (OUTLIER) cc_final: 0.7882 (p) REVERT: D 76 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8380 (mp) REVERT: D 161 ASP cc_start: 0.7150 (p0) cc_final: 0.6941 (p0) REVERT: D 272 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8596 (tm-30) outliers start: 52 outliers final: 38 residues processed: 241 average time/residue: 0.5291 time to fit residues: 140.8439 Evaluate side-chains 260 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 282 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 28 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 GLN E 193 GLN B 101 GLN C 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104231 restraints weight = 14674.175| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.30 r_work: 0.2871 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13845 Z= 0.180 Angle : 0.565 5.755 18730 Z= 0.294 Chirality : 0.045 0.153 2100 Planarity : 0.004 0.035 2275 Dihedral : 16.325 110.079 2432 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.14 % Allowed : 12.93 % Favored : 81.93 % 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: 0.93 (0.21), residues: 1550 helix: 2.78 (0.21), residues: 515 sheet: 0.02 (0.24), residues: 375 loop : -0.79 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 109 TYR 0.007 0.001 TYR D 197 PHE 0.013 0.001 PHE A 37 TRP 0.007 0.001 TRP D 47 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00433 (13845) covalent geometry : angle 0.56501 (18730) hydrogen bonds : bond 0.07748 ( 590) hydrogen bonds : angle 4.71118 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 210 time to evaluate : 0.540 Fit side-chains REVERT: A 44 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 91 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7408 (t0) REVERT: A 189 ARG cc_start: 0.7868 (mtp-110) cc_final: 0.7502 (mtp85) REVERT: A 243 GLU cc_start: 0.8854 (tp30) cc_final: 0.8613 (tp30) REVERT: A 272 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8610 (tm-30) REVERT: E 44 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7721 (p) REVERT: E 76 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8536 (mp) REVERT: E 88 ASP cc_start: 0.7153 (m-30) cc_final: 0.6479 (t0) REVERT: E 272 GLU cc_start: 0.9280 (tm-30) cc_final: 0.8483 (tm-30) REVERT: B 161 ASP cc_start: 0.7059 (p0) cc_final: 0.6830 (p0) REVERT: B 272 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8564 (tm-30) REVERT: C 44 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.7828 (p) REVERT: C 272 GLU cc_start: 0.9282 (tm-30) cc_final: 0.8644 (tm-30) REVERT: D 76 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8442 (mp) REVERT: D 101 GLN cc_start: 0.7301 (mm-40) cc_final: 0.7091 (mm-40) REVERT: D 161 ASP cc_start: 0.7234 (p0) cc_final: 0.6955 (p0) REVERT: D 272 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8617 (tm-30) outliers start: 72 outliers final: 52 residues processed: 243 average time/residue: 0.5461 time to fit residues: 146.1925 Evaluate side-chains 258 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 118 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 0.0270 chunk 38 optimal weight: 4.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 GLN E 193 GLN C 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.181248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106967 restraints weight = 14641.952| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.31 r_work: 0.2954 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13845 Z= 0.129 Angle : 0.537 6.444 18730 Z= 0.279 Chirality : 0.044 0.159 2100 Planarity : 0.004 0.062 2275 Dihedral : 15.641 117.490 2432 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.43 % Allowed : 14.00 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.21), residues: 1550 helix: 3.00 (0.21), residues: 520 sheet: 0.09 (0.24), residues: 375 loop : -0.72 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 109 TYR 0.006 0.001 TYR A 251 PHE 0.012 0.001 PHE E 37 TRP 0.007 0.001 TRP D 47 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00291 (13845) covalent geometry : angle 0.53665 (18730) hydrogen bonds : bond 0.06118 ( 590) hydrogen bonds : angle 4.41672 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 0.392 Fit side-chains REVERT: A 44 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7761 (p) REVERT: A 91 ASP cc_start: 0.7653 (p0) cc_final: 0.7388 (t0) REVERT: A 189 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7521 (mtp85) REVERT: A 243 GLU cc_start: 0.8824 (tp30) cc_final: 0.8584 (tp30) REVERT: A 272 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8655 (tm-30) REVERT: E 44 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7793 (p) REVERT: E 76 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8515 (mp) REVERT: E 88 ASP cc_start: 0.7090 (m-30) cc_final: 0.6590 (t0) REVERT: E 161 ASP cc_start: 0.7262 (p0) cc_final: 0.7037 (p0) REVERT: E 272 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8434 (tm-30) REVERT: B 161 ASP cc_start: 0.7008 (p0) cc_final: 0.6773 (p0) REVERT: C 44 SER cc_start: 0.8297 (OUTLIER) cc_final: 0.7871 (p) REVERT: D 35 GLU cc_start: 0.8788 (tp30) cc_final: 0.8460 (mm-30) REVERT: D 76 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8442 (mp) REVERT: D 101 GLN cc_start: 0.7274 (mm-40) cc_final: 0.7052 (mm-40) REVERT: D 118 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6276 (mtp180) REVERT: D 161 ASP cc_start: 0.7159 (p0) cc_final: 0.6929 (p0) REVERT: D 272 GLU cc_start: 0.9252 (tm-30) cc_final: 0.8663 (tm-30) outliers start: 62 outliers final: 47 residues processed: 247 average time/residue: 0.4713 time to fit residues: 128.7547 Evaluate side-chains 266 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 213 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 145 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 GLN E 193 GLN B 101 GLN C 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.179570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103302 restraints weight = 14457.657| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.30 r_work: 0.2875 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13845 Z= 0.186 Angle : 0.573 5.794 18730 Z= 0.299 Chirality : 0.045 0.148 2100 Planarity : 0.004 0.056 2275 Dihedral : 15.941 127.343 2432 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.07 % Allowed : 13.64 % Favored : 81.29 % 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: 0.83 (0.21), residues: 1550 helix: 2.79 (0.21), residues: 515 sheet: -0.25 (0.24), residues: 400 loop : -0.80 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 109 TYR 0.020 0.001 TYR B 102 PHE 0.013 0.001 PHE C 37 TRP 0.007 0.001 TRP D 47 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00449 (13845) covalent geometry : angle 0.57257 (18730) hydrogen bonds : bond 0.07707 ( 590) hydrogen bonds : angle 4.64297 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 203 time to evaluate : 0.540 Fit side-chains REVERT: A 44 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7771 (p) REVERT: A 91 ASP cc_start: 0.7667 (p0) cc_final: 0.7428 (t0) REVERT: A 189 ARG cc_start: 0.7907 (mtp-110) cc_final: 0.7555 (mtp85) REVERT: A 272 GLU cc_start: 0.9276 (tm-30) cc_final: 0.8781 (tm-30) REVERT: E 35 GLU cc_start: 0.8719 (tp30) cc_final: 0.8427 (mm-30) REVERT: E 44 SER cc_start: 0.8192 (OUTLIER) cc_final: 0.7701 (p) REVERT: E 76 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8515 (mp) REVERT: E 88 ASP cc_start: 0.7145 (m-30) cc_final: 0.6627 (t0) REVERT: E 272 GLU cc_start: 0.9296 (tm-30) cc_final: 0.8598 (tm-30) REVERT: B 161 ASP cc_start: 0.7145 (p0) cc_final: 0.6900 (p0) REVERT: C 44 SER cc_start: 0.8285 (OUTLIER) cc_final: 0.7810 (p) REVERT: D 76 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8457 (mp) REVERT: D 88 ASP cc_start: 0.7021 (m-30) cc_final: 0.6279 (m-30) REVERT: D 101 GLN cc_start: 0.7303 (mm-40) cc_final: 0.7082 (mm-40) REVERT: D 161 ASP cc_start: 0.7286 (p0) cc_final: 0.7003 (p0) REVERT: D 252 MET cc_start: 0.8641 (mmm) cc_final: 0.8415 (mmp) outliers start: 71 outliers final: 58 residues processed: 239 average time/residue: 0.4868 time to fit residues: 129.1131 Evaluate side-chains 263 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 200 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 126 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 GLN E 193 GLN C 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.182656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107945 restraints weight = 14707.205| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.33 r_work: 0.3007 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13845 Z= 0.127 Angle : 0.544 5.720 18730 Z= 0.283 Chirality : 0.044 0.140 2100 Planarity : 0.004 0.052 2275 Dihedral : 15.332 132.627 2432 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.14 % Allowed : 14.50 % Favored : 81.36 % 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: 1.06 (0.21), residues: 1550 helix: 3.01 (0.21), residues: 520 sheet: -0.10 (0.24), residues: 400 loop : -0.73 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 109 TYR 0.007 0.001 TYR C 254 PHE 0.012 0.001 PHE D 37 TRP 0.007 0.001 TRP D 47 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00287 (13845) covalent geometry : angle 0.54402 (18730) hydrogen bonds : bond 0.05953 ( 590) hydrogen bonds : angle 4.33896 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 0.480 Fit side-chains REVERT: A 35 GLU cc_start: 0.8588 (tp30) cc_final: 0.8216 (tm-30) REVERT: A 44 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.7798 (p) REVERT: A 189 ARG cc_start: 0.7884 (mtp-110) cc_final: 0.7550 (mtp85) REVERT: A 243 GLU cc_start: 0.8790 (tp30) cc_final: 0.8535 (tp30) REVERT: A 272 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8638 (tm-30) REVERT: E 35 GLU cc_start: 0.8668 (tp30) cc_final: 0.8388 (mm-30) REVERT: E 44 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7795 (p) REVERT: E 76 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8529 (mp) REVERT: E 88 ASP cc_start: 0.7126 (m-30) cc_final: 0.6618 (t0) REVERT: E 161 ASP cc_start: 0.7279 (p0) cc_final: 0.7060 (p0) REVERT: E 272 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8498 (tm-30) REVERT: B 161 ASP cc_start: 0.7043 (p0) cc_final: 0.6802 (p0) REVERT: C 44 SER cc_start: 0.8325 (OUTLIER) cc_final: 0.7872 (p) REVERT: D 35 GLU cc_start: 0.8732 (tp30) cc_final: 0.8484 (tm-30) REVERT: D 75 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7787 (mm-30) REVERT: D 76 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8438 (mp) REVERT: D 88 ASP cc_start: 0.7014 (m-30) cc_final: 0.6294 (m-30) REVERT: D 118 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6246 (mtp180) REVERT: D 161 ASP cc_start: 0.7164 (p0) cc_final: 0.6945 (p0) outliers start: 58 outliers final: 47 residues processed: 247 average time/residue: 0.4714 time to fit residues: 129.6707 Evaluate side-chains 264 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 211 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 40 ASN E 101 GLN E 193 GLN C 101 GLN D 40 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.179628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.104967 restraints weight = 14612.743| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.30 r_work: 0.2893 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13845 Z= 0.193 Angle : 0.588 5.786 18730 Z= 0.307 Chirality : 0.045 0.152 2100 Planarity : 0.004 0.050 2275 Dihedral : 15.747 134.870 2432 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.21 % Allowed : 14.64 % Favored : 81.14 % 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: 0.88 (0.21), residues: 1550 helix: 2.81 (0.21), residues: 515 sheet: -0.15 (0.24), residues: 400 loop : -0.80 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 109 TYR 0.018 0.001 TYR C 102 PHE 0.012 0.001 PHE D 312 TRP 0.007 0.002 TRP C 72 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00473 (13845) covalent geometry : angle 0.58752 (18730) hydrogen bonds : bond 0.07607 ( 590) hydrogen bonds : angle 4.58575 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 192 time to evaluate : 0.349 Fit side-chains REVERT: A 35 GLU cc_start: 0.8628 (tp30) cc_final: 0.8359 (tm-30) REVERT: A 44 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.7757 (p) REVERT: A 189 ARG cc_start: 0.7872 (mtp-110) cc_final: 0.7522 (mtp85) REVERT: A 272 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8623 (tm-30) REVERT: E 44 SER cc_start: 0.8168 (OUTLIER) cc_final: 0.7653 (p) REVERT: E 76 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8486 (mp) REVERT: E 88 ASP cc_start: 0.7115 (m-30) cc_final: 0.6599 (t0) REVERT: E 272 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8613 (tm-30) REVERT: B 35 GLU cc_start: 0.8602 (tp30) cc_final: 0.8220 (tm-30) REVERT: B 161 ASP cc_start: 0.7087 (p0) cc_final: 0.6866 (p0) REVERT: B 272 GLU cc_start: 0.9239 (tm-30) cc_final: 0.8568 (tm-30) REVERT: C 44 SER cc_start: 0.8081 (OUTLIER) cc_final: 0.7626 (p) REVERT: D 35 GLU cc_start: 0.8791 (tp30) cc_final: 0.8474 (mm-30) REVERT: D 75 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7806 (mm-30) REVERT: D 76 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8405 (mp) REVERT: D 88 ASP cc_start: 0.6960 (m-30) cc_final: 0.6231 (m-30) REVERT: D 101 GLN cc_start: 0.7283 (mm-40) cc_final: 0.7056 (mm-40) REVERT: D 161 ASP cc_start: 0.7190 (p0) cc_final: 0.6923 (p0) outliers start: 59 outliers final: 50 residues processed: 225 average time/residue: 0.4637 time to fit residues: 115.7864 Evaluate side-chains 245 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 190 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 243 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 49 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 GLN E 193 GLN C 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.183305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108698 restraints weight = 14683.378| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.33 r_work: 0.2953 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13845 Z= 0.117 Angle : 0.541 5.702 18730 Z= 0.282 Chirality : 0.044 0.151 2100 Planarity : 0.004 0.050 2275 Dihedral : 15.067 134.702 2432 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.93 % Allowed : 14.93 % Favored : 81.14 % 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: 1.20 (0.21), residues: 1550 helix: 3.40 (0.21), residues: 495 sheet: -0.09 (0.23), residues: 425 loop : -0.70 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 109 TYR 0.018 0.001 TYR C 102 PHE 0.011 0.001 PHE E 37 TRP 0.007 0.001 TRP D 47 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00252 (13845) covalent geometry : angle 0.54072 (18730) hydrogen bonds : bond 0.05650 ( 590) hydrogen bonds : angle 4.28185 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5249.88 seconds wall clock time: 89 minutes 51.89 seconds (5391.89 seconds total)