Starting phenix.real_space_refine on Fri Jul 3 14:20:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oq6_17106/07_2026/8oq6_17106.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oq6_17106/07_2026/8oq6_17106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oq6_17106/07_2026/8oq6_17106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oq6_17106/07_2026/8oq6_17106.map" model { file = "/net/cci-nas-00/data/ceres_data/8oq6_17106/07_2026/8oq6_17106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oq6_17106/07_2026/8oq6_17106.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8oq6_17106/07_2026/8oq6_17106.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oq6_17106/07_2026/8oq6_17106.cif" } resolution = 3.21 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 S 75 5.16 5 Cl 2 4.86 5 C 9485 2.51 5 N 2240 2.21 5 O 2665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14477 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2750 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2750 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2750 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2750 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2750 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 132 Unusual residues: {' CL': 2, '7P9': 2, 'D10': 3, 'NAG': 2, 'OCT': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 130 Unusual residues: {'7P9': 2, 'D10': 3, 'NAG': 2, 'OCT': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 130 Unusual residues: {'7P9': 2, 'D10': 3, 'NAG': 2, 'OCT': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 130 Unusual residues: {'7P9': 2, 'D10': 3, 'NAG': 2, 'OCT': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 130 Unusual residues: {'7P9': 2, 'D10': 3, 'NAG': 2, 'OCT': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 3.24, per 1000 atoms: 0.22 Number of scatterers: 14477 At special positions: 0 Unit cell: (93.6945, 94.359, 136.887, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 75 16.00 P 10 15.00 O 2665 8.00 N 2240 7.00 C 9485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 212 " distance=2.03 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 Atom "HETATM14178 O5 NAG D 503 .*. O " rejected from bonding due to valence issues. Atom "HETATM13776 O5 NAG A 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14308 O5 NAG E 503 .*. O " rejected from bonding due to valence issues. Atom "HETATM14048 O5 NAG C 503 .*. O " rejected from bonding due to valence issues. Atom "HETATM13918 O5 NAG B 503 .*. O " rejected from bonding due to valence issues. Atom "HETATM13762 O5 NAG A 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM13904 O5 NAG B 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14034 O5 NAG C 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14164 O5 NAG D 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14294 O5 NAG E 502 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 140 " " NAG A 502 " - " ASN A 234 " " NAG B 502 " - " ASN B 140 " " NAG B 503 " - " ASN B 234 " " NAG C 502 " - " ASN C 140 " " NAG C 503 " - " ASN C 234 " " NAG D 502 " - " ASN D 140 " " NAG D 503 " - " ASN D 234 " " NAG E 502 " - " ASN E 140 " " NAG E 503 " - " ASN E 234 " Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 609.7 milliseconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 41.1% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 146 through 153 removed outlier: 4.026A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 280 through 300 removed outlier: 3.801A pdb=" N PHE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.553A pdb=" N TRP A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 309 through 334 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 342 through 380 removed outlier: 3.789A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 478 removed outlier: 3.930A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'B' and resid 74 through 78 Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 146 through 153 removed outlier: 4.026A pdb=" N LYS B 151 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 280 through 300 removed outlier: 3.801A pdb=" N PHE B 284 " --> pdb=" O HIS B 280 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.554A pdb=" N TRP B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 309 through 334 Proline residue: B 315 - end of helix Processing helix chain 'B' and resid 342 through 380 removed outlier: 3.789A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 478 removed outlier: 3.929A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 131 through 134 Processing helix chain 'C' and resid 146 through 153 removed outlier: 4.026A pdb=" N LYS C 151 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 280 through 300 removed outlier: 3.801A pdb=" N PHE C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.554A pdb=" N TRP C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 309 through 334 Proline residue: C 315 - end of helix Processing helix chain 'C' and resid 342 through 380 removed outlier: 3.789A pdb=" N TYR C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 478 removed outlier: 3.930A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Proline residue: C 464 - end of helix Processing helix chain 'D' and resid 74 through 78 Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 146 through 153 removed outlier: 4.025A pdb=" N LYS D 151 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 Processing helix chain 'D' and resid 280 through 300 removed outlier: 3.802A pdb=" N PHE D 284 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.553A pdb=" N TRP D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 309 through 334 Proline residue: D 315 - end of helix Processing helix chain 'D' and resid 342 through 380 removed outlier: 3.788A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 478 removed outlier: 3.929A pdb=" N ILE D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Proline residue: D 464 - end of helix Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 146 through 153 removed outlier: 4.025A pdb=" N LYS E 151 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 280 through 300 removed outlier: 3.801A pdb=" N PHE E 284 " --> pdb=" O HIS E 280 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.554A pdb=" N TRP E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 309 through 334 Proline residue: E 315 - end of helix Processing helix chain 'E' and resid 342 through 380 removed outlier: 3.790A pdb=" N TYR E 362 " --> pdb=" O SER E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 478 removed outlier: 3.929A pdb=" N ILE E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 145 removed outlier: 3.957A pdb=" N SER A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A 121 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU A 108 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N TYR A 123 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLU A 106 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ARG A 125 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLN A 104 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR A 127 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ASP A 102 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N LYS A 129 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N GLY A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 removed outlier: 6.941A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE A 168 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG A 191 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A 121 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU A 108 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N TYR A 123 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLU A 106 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ARG A 125 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLN A 104 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR A 127 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ASP A 102 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N LYS A 129 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N GLY A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.653A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER A 218 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN A 269 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR A 276 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU A 252 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ARG A 278 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE A 250 " --> pdb=" O ARG A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 145 removed outlier: 3.957A pdb=" N SER B 110 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR B 121 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU B 108 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N TYR B 123 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU B 106 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ARG B 125 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLN B 104 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR B 127 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASP B 102 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N LYS B 129 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N GLY B 100 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 168 removed outlier: 6.941A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE B 168 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG B 191 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER B 110 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR B 121 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU B 108 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N TYR B 123 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU B 106 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ARG B 125 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLN B 104 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR B 127 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASP B 102 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N LYS B 129 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N GLY B 100 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.653A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER B 218 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN B 269 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 276 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU B 252 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ARG B 278 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE B 250 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.957A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR C 121 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU C 108 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N TYR C 123 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU C 106 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ARG C 125 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLN C 104 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR C 127 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ASP C 102 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N LYS C 129 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N GLY C 100 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 163 through 168 removed outlier: 6.942A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE C 168 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ARG C 191 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR C 121 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU C 108 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N TYR C 123 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU C 106 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ARG C 125 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLN C 104 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR C 127 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ASP C 102 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N LYS C 129 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N GLY C 100 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.653A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER C 218 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN C 269 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR C 276 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU C 252 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ARG C 278 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE C 250 " --> pdb=" O ARG C 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 143 through 145 removed outlier: 3.957A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR D 121 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU D 108 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N TYR D 123 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLU D 106 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ARG D 125 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLN D 104 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR D 127 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASP D 102 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N LYS D 129 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N GLY D 100 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 163 through 168 removed outlier: 6.941A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE D 168 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ARG D 191 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR D 121 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU D 108 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N TYR D 123 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLU D 106 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ARG D 125 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLN D 104 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR D 127 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASP D 102 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N LYS D 129 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N GLY D 100 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.653A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER D 218 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN D 269 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR D 276 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU D 252 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ARG D 278 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE D 250 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 145 removed outlier: 3.957A pdb=" N SER E 110 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR E 121 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU E 108 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N TYR E 123 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU E 106 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ARG E 125 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLN E 104 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR E 127 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASP E 102 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N LYS E 129 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N GLY E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.941A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE E 168 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG E 191 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER E 110 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR E 121 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU E 108 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N TYR E 123 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU E 106 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ARG E 125 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLN E 104 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR E 127 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASP E 102 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N LYS E 129 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N GLY E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.653A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER E 218 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN E 269 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR E 276 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLU E 252 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ARG E 278 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE E 250 " --> pdb=" O ARG E 278 " (cutoff:3.500A) 790 hydrogen bonds defined for protein. 2145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2120 1.31 - 1.44: 4365 1.44 - 1.56: 8095 1.56 - 1.69: 20 1.69 - 1.81: 140 Bond restraints: 14740 Sorted by residual: bond pdb=" O3 7P9 B 507 " pdb=" P1 7P9 B 507 " ideal model delta sigma weight residual 1.526 1.647 -0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" O3 7P9 E 508 " pdb=" P1 7P9 E 508 " ideal model delta sigma weight residual 1.526 1.647 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" O3 7P9 E 507 " pdb=" P1 7P9 E 507 " ideal model delta sigma weight residual 1.526 1.647 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" O3 7P9 A 506 " pdb=" P1 7P9 A 506 " ideal model delta sigma weight residual 1.526 1.647 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" O3 7P9 D 508 " pdb=" P1 7P9 D 508 " ideal model delta sigma weight residual 1.526 1.647 -0.121 2.00e-02 2.50e+03 3.66e+01 ... (remaining 14735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 19282 1.85 - 3.70: 297 3.70 - 5.55: 247 5.55 - 7.41: 43 7.41 - 9.26: 36 Bond angle restraints: 19905 Sorted by residual: angle pdb=" O1 7P9 E 507 " pdb=" P1 7P9 E 507 " pdb=" O4 7P9 E 507 " ideal model delta sigma weight residual 100.59 109.85 -9.26 3.00e+00 1.11e-01 9.52e+00 angle pdb=" O1 7P9 B 507 " pdb=" P1 7P9 B 507 " pdb=" O4 7P9 B 507 " ideal model delta sigma weight residual 100.59 109.82 -9.23 3.00e+00 1.11e-01 9.46e+00 angle pdb=" O1 7P9 A 506 " pdb=" P1 7P9 A 506 " pdb=" O4 7P9 A 506 " ideal model delta sigma weight residual 100.59 109.81 -9.22 3.00e+00 1.11e-01 9.45e+00 angle pdb=" O1 7P9 D 507 " pdb=" P1 7P9 D 507 " pdb=" O4 7P9 D 507 " ideal model delta sigma weight residual 100.59 109.78 -9.19 3.00e+00 1.11e-01 9.39e+00 angle pdb=" O1 7P9 C 507 " pdb=" P1 7P9 C 507 " pdb=" O4 7P9 C 507 " ideal model delta sigma weight residual 100.59 109.78 -9.19 3.00e+00 1.11e-01 9.39e+00 ... (remaining 19900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.33: 8369 22.33 - 44.66: 256 44.66 - 66.99: 95 66.99 - 89.32: 0 89.32 - 111.65: 5 Dihedral angle restraints: 8725 sinusoidal: 3710 harmonic: 5015 Sorted by residual: dihedral pdb=" C11 7P9 B 507 " pdb=" C18 7P9 B 507 " pdb=" C19 7P9 B 507 " pdb=" C17 7P9 B 507 " ideal model delta sinusoidal sigma weight residual 180.47 68.82 111.65 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C11 7P9 D 507 " pdb=" C18 7P9 D 507 " pdb=" C19 7P9 D 507 " pdb=" C17 7P9 D 507 " ideal model delta sinusoidal sigma weight residual 180.47 68.84 111.63 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C11 7P9 A 506 " pdb=" C18 7P9 A 506 " pdb=" C19 7P9 A 506 " pdb=" C17 7P9 A 506 " ideal model delta sinusoidal sigma weight residual 180.47 68.86 111.61 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 8722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.271: 2240 0.271 - 0.542: 0 0.542 - 0.813: 0 0.813 - 1.084: 0 1.084 - 1.355: 5 Chirality restraints: 2245 Sorted by residual: chirality pdb=" C1 NAG E 503 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 503 " pdb=" O5 NAG E 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.04 -1.36 2.00e-01 2.50e+01 4.59e+01 chirality pdb=" C1 NAG C 503 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 503 " pdb=" O5 NAG C 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-01 2.50e+01 4.58e+01 chirality pdb=" C1 NAG B 503 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B 503 " pdb=" O5 NAG B 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-01 2.50e+01 4.58e+01 ... (remaining 2242 not shown) Planarity restraints: 2405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " 0.048 2.00e-02 2.50e+03 1.60e-01 3.19e+02 pdb=" CG ASN C 234 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " 0.100 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " -0.283 2.00e-02 2.50e+03 pdb=" C1 NAG C 503 " 0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.048 2.00e-02 2.50e+03 1.60e-01 3.18e+02 pdb=" CG ASN D 234 " -0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " 0.100 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.283 2.00e-02 2.50e+03 pdb=" C1 NAG D 503 " 0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.048 2.00e-02 2.50e+03 1.60e-01 3.18e+02 pdb=" CG ASN A 234 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.100 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.283 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " -0.181 2.00e-02 2.50e+03 ... (remaining 2402 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3019 2.79 - 3.32: 12357 3.32 - 3.84: 22397 3.84 - 4.37: 26679 4.37 - 4.90: 48880 Nonbonded interactions: 113332 Sorted by model distance: nonbonded pdb=" OG SER D 166 " pdb=" O HOH D 601 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP E 117 " pdb=" O HOH E 601 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASP B 117 " pdb=" O HOH B 601 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASP D 117 " pdb=" O HOH D 602 " model vdw 2.279 3.040 nonbonded pdb=" OD1 ASP A 117 " pdb=" O HOH A 601 " model vdw 2.279 3.040 ... (remaining 113327 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 74 through 479 or resid 502 or resid 505 or resid 507)) selection = (chain 'B' and (resid 74 through 479 or resid 502 or resid 505 or resid 507)) selection = (chain 'C' and (resid 74 through 479 or resid 502 or resid 505 or resid 507)) selection = (chain 'D' and (resid 74 through 479 or resid 502 or resid 505 or resid 507)) selection = (chain 'E' and (resid 74 through 479 or resid 502 or resid 505 or resid 507)) } 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: 5.170 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.270 Find NCS groups from input model: 0.400 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 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 : 0.006 0.131 14755 Z= 0.326 Angle : 1.419 45.344 19945 Z= 0.507 Chirality : 0.075 1.355 2245 Planarity : 0.003 0.026 2395 Dihedral : 12.318 111.651 5450 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.21), residues: 1660 helix: 2.38 (0.23), residues: 570 sheet: 1.96 (0.25), residues: 440 loop : 1.26 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 313 TYR 0.012 0.002 TYR D 340 PHE 0.010 0.001 PHE E 290 TRP 0.008 0.001 TRP D 349 HIS 0.004 0.001 HIS D 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.30 (14740) covalent geometry : angle 0.84898 / 0.34 (19905) SS BOND : bond 0.00107 / 0.06 ( 5) SS BOND : angle 0.63330 / 0.36 ( 10) hydrogen bonds : bond 0.17535 / 11.43 ( 715) hydrogen bonds : angle 6.30753 / 4.33 ( 2145) link_NAG-ASN : bond 0.10502 / 6.92 ( 10) link_NAG-ASN : angle 29.34641 / 20.60 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.540 Fit side-chains REVERT: A 88 MET cc_start: 0.8016 (ptp) cc_final: 0.7794 (ptm) REVERT: A 148 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7795 (mtm-85) REVERT: A 157 ASP cc_start: 0.8532 (p0) cc_final: 0.8052 (p0) REVERT: A 238 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7543 (mtmm) REVERT: B 88 MET cc_start: 0.8111 (ptp) cc_final: 0.7887 (ptm) REVERT: B 238 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7197 (mtmm) REVERT: B 335 MET cc_start: 0.7179 (mtm) cc_final: 0.6948 (mmt) REVERT: C 129 LYS cc_start: 0.8721 (tttt) cc_final: 0.8447 (ttmt) REVERT: C 157 ASP cc_start: 0.8463 (p0) cc_final: 0.7844 (p0) REVERT: C 164 LYS cc_start: 0.8857 (mttt) cc_final: 0.8627 (mttm) REVERT: C 238 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7398 (mtmm) REVERT: C 247 GLN cc_start: 0.7964 (pm20) cc_final: 0.7759 (pt0) REVERT: C 335 MET cc_start: 0.6953 (mtm) cc_final: 0.6715 (mmt) REVERT: D 129 LYS cc_start: 0.8686 (tttt) cc_final: 0.8422 (ttmt) REVERT: D 148 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7842 (mtm-85) REVERT: D 157 ASP cc_start: 0.8418 (p0) cc_final: 0.7829 (p0) REVERT: D 238 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7323 (mtmm) REVERT: D 247 GLN cc_start: 0.7976 (pm20) cc_final: 0.7723 (pt0) REVERT: D 361 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8505 (tm-30) REVERT: E 129 LYS cc_start: 0.8598 (tttt) cc_final: 0.8386 (ttmt) REVERT: E 157 ASP cc_start: 0.8476 (p0) cc_final: 0.8025 (p0) REVERT: E 238 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7440 (mtmm) REVERT: E 361 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8521 (tm-30) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1655 time to fit residues: 71.6350 Evaluate side-chains 240 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 GLN B 251 GLN B 287 GLN C 251 GLN C 287 GLN D 251 GLN E 251 GLN E 287 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.128572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.094901 restraints weight = 15579.336| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.94 r_work: 0.2747 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14755 Z= 0.188 Angle : 0.610 6.956 19945 Z= 0.313 Chirality : 0.044 0.164 2245 Planarity : 0.005 0.031 2395 Dihedral : 13.547 93.471 2300 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.84 % Allowed : 6.36 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.21), residues: 1660 helix: 2.01 (0.22), residues: 580 sheet: 1.39 (0.24), residues: 475 loop : 0.99 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 337 TYR 0.025 0.002 TYR E 272 PHE 0.013 0.002 PHE A 159 TRP 0.010 0.001 TRP D 349 HIS 0.005 0.002 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (14740) covalent geometry : angle 0.59038 / 0.31 (19905) SS BOND : bond 0.00376 / 0.21 ( 5) SS BOND : angle 1.40819 / 0.80 ( 10) hydrogen bonds : bond 0.06783 / 4.47 ( 715) hydrogen bonds : angle 4.24040 / 2.91 ( 2145) link_NAG-ASN : bond 0.00561 / 0.37 ( 10) link_NAG-ASN : angle 3.94507 / 2.55 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 252 time to evaluate : 0.575 Fit side-chains REVERT: A 88 MET cc_start: 0.8485 (ptp) cc_final: 0.8167 (ptt) REVERT: A 238 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7448 (mtmm) REVERT: B 88 MET cc_start: 0.8659 (ptp) cc_final: 0.8331 (ptm) REVERT: B 278 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7890 (ttm170) REVERT: B 335 MET cc_start: 0.7064 (mtm) cc_final: 0.6225 (mmt) REVERT: C 129 LYS cc_start: 0.8857 (tttt) cc_final: 0.8565 (ttmt) REVERT: C 238 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7741 (ttmm) REVERT: C 247 GLN cc_start: 0.8252 (pm20) cc_final: 0.7945 (pt0) REVERT: C 252 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7209 (mm-30) REVERT: C 335 MET cc_start: 0.7055 (mtm) cc_final: 0.6153 (mmt) REVERT: C 337 ARG cc_start: 0.7380 (mmt-90) cc_final: 0.7134 (mmt-90) REVERT: D 247 GLN cc_start: 0.8253 (pm20) cc_final: 0.7887 (pt0) REVERT: D 337 ARG cc_start: 0.7303 (mmt90) cc_final: 0.6784 (mmt-90) outliers start: 28 outliers final: 26 residues processed: 276 average time/residue: 0.1451 time to fit residues: 55.1565 Evaluate side-chains 258 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.130068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.094157 restraints weight = 15467.283| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.10 r_work: 0.2730 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14755 Z= 0.170 Angle : 0.544 5.208 19945 Z= 0.285 Chirality : 0.043 0.160 2245 Planarity : 0.004 0.035 2395 Dihedral : 12.751 76.903 2300 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.10 % Allowed : 8.39 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.88 (0.21), residues: 1660 helix: 2.01 (0.23), residues: 580 sheet: 0.96 (0.25), residues: 440 loop : 0.92 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 337 TYR 0.023 0.002 TYR D 272 PHE 0.011 0.002 PHE A 159 TRP 0.010 0.001 TRP D 349 HIS 0.005 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (14740) covalent geometry : angle 0.53732 / 0.28 (19905) SS BOND : bond 0.00259 / 0.14 ( 5) SS BOND : angle 1.13205 / 0.64 ( 10) hydrogen bonds : bond 0.06497 / 4.28 ( 715) hydrogen bonds : angle 4.00069 / 2.75 ( 2145) link_NAG-ASN : bond 0.00273 / 0.18 ( 10) link_NAG-ASN : angle 2.18944 / 1.48 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.562 Fit side-chains REVERT: A 88 MET cc_start: 0.8400 (ptp) cc_final: 0.8089 (ptt) REVERT: A 278 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7667 (mtt90) REVERT: B 88 MET cc_start: 0.8626 (ptp) cc_final: 0.8283 (ptt) REVERT: B 106 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: B 157 ASP cc_start: 0.8837 (p0) cc_final: 0.8128 (p0) REVERT: B 278 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7810 (ttm170) REVERT: B 335 MET cc_start: 0.6715 (mtm) cc_final: 0.6453 (mmt) REVERT: C 92 PHE cc_start: 0.8349 (t80) cc_final: 0.8089 (t80) REVERT: C 247 GLN cc_start: 0.8336 (pm20) cc_final: 0.7973 (pt0) REVERT: C 252 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7180 (mm-30) REVERT: C 278 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7889 (ptp90) REVERT: C 335 MET cc_start: 0.7106 (mtm) cc_final: 0.6117 (mmt) REVERT: D 157 ASP cc_start: 0.8835 (p0) cc_final: 0.8184 (p0) REVERT: D 247 GLN cc_start: 0.8341 (pm20) cc_final: 0.7948 (pt0) REVERT: D 337 ARG cc_start: 0.7331 (mmt90) cc_final: 0.6722 (mmt-90) REVERT: E 157 ASP cc_start: 0.8866 (p0) cc_final: 0.8254 (p0) REVERT: E 337 ARG cc_start: 0.7379 (mmt90) cc_final: 0.6698 (mmt-90) outliers start: 32 outliers final: 25 residues processed: 260 average time/residue: 0.1488 time to fit residues: 53.2013 Evaluate side-chains 255 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.129130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.093346 restraints weight = 15493.996| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.10 r_work: 0.2714 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14755 Z= 0.181 Angle : 0.556 5.348 19945 Z= 0.294 Chirality : 0.044 0.195 2245 Planarity : 0.004 0.035 2395 Dihedral : 12.476 60.708 2300 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.82 % Allowed : 9.05 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.61 (0.21), residues: 1660 helix: 1.98 (0.23), residues: 580 sheet: 0.77 (0.23), residues: 475 loop : 0.57 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.023 0.002 TYR D 272 PHE 0.013 0.002 PHE A 159 TRP 0.011 0.001 TRP D 349 HIS 0.005 0.002 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (14740) covalent geometry : angle 0.55158 / 0.29 (19905) SS BOND : bond 0.00243 / 0.13 ( 5) SS BOND : angle 1.12159 / 0.64 ( 10) hydrogen bonds : bond 0.06564 / 4.32 ( 715) hydrogen bonds : angle 3.98253 / 2.74 ( 2145) link_NAG-ASN : bond 0.00362 / 0.25 ( 10) link_NAG-ASN : angle 1.80182 / 1.23 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.444 Fit side-chains REVERT: A 88 MET cc_start: 0.8401 (ptp) cc_final: 0.8089 (ptt) REVERT: A 278 ARG cc_start: 0.8130 (ttm170) cc_final: 0.7599 (mtt90) REVERT: A 337 ARG cc_start: 0.7600 (mmt-90) cc_final: 0.7145 (mmt-90) REVERT: B 88 MET cc_start: 0.8617 (ptp) cc_final: 0.8282 (ptt) REVERT: B 106 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: B 157 ASP cc_start: 0.8860 (p0) cc_final: 0.8139 (p0) REVERT: B 278 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7818 (ttm170) REVERT: B 335 MET cc_start: 0.7282 (mtm) cc_final: 0.6144 (mmt) REVERT: B 337 ARG cc_start: 0.7483 (mmt90) cc_final: 0.6818 (mmt-90) REVERT: C 157 ASP cc_start: 0.8846 (p0) cc_final: 0.8203 (p0) REVERT: C 247 GLN cc_start: 0.8425 (pm20) cc_final: 0.8017 (pt0) REVERT: C 252 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7343 (mm-30) REVERT: C 278 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7665 (mtt90) REVERT: C 335 MET cc_start: 0.6813 (mtm) cc_final: 0.5934 (mmt) REVERT: D 92 PHE cc_start: 0.8464 (t80) cc_final: 0.8231 (t80) REVERT: D 157 ASP cc_start: 0.8837 (p0) cc_final: 0.8119 (p0) REVERT: D 247 GLN cc_start: 0.8437 (pm20) cc_final: 0.7996 (pt0) REVERT: D 337 ARG cc_start: 0.7298 (mmt90) cc_final: 0.6677 (mmt-90) REVERT: E 157 ASP cc_start: 0.8870 (p0) cc_final: 0.8159 (p0) REVERT: E 337 ARG cc_start: 0.7355 (mmt90) cc_final: 0.6680 (mmt-90) outliers start: 43 outliers final: 34 residues processed: 264 average time/residue: 0.1412 time to fit residues: 51.4322 Evaluate side-chains 263 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 79 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.133437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.099262 restraints weight = 15250.256| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.10 r_work: 0.2725 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14755 Z= 0.177 Angle : 0.538 5.216 19945 Z= 0.286 Chirality : 0.043 0.169 2245 Planarity : 0.004 0.060 2395 Dihedral : 12.348 59.253 2300 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.69 % Allowed : 9.77 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.52 (0.21), residues: 1660 helix: 2.00 (0.23), residues: 580 sheet: 0.74 (0.25), residues: 420 loop : 0.42 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 337 TYR 0.022 0.002 TYR D 272 PHE 0.012 0.002 PHE E 159 TRP 0.011 0.001 TRP D 349 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (14740) covalent geometry : angle 0.53518 / 0.29 (19905) SS BOND : bond 0.00223 / 0.12 ( 5) SS BOND : angle 1.02140 / 0.58 ( 10) hydrogen bonds : bond 0.06455 / 4.25 ( 715) hydrogen bonds : angle 3.93925 / 2.71 ( 2145) link_NAG-ASN : bond 0.00389 / 0.26 ( 10) link_NAG-ASN : angle 1.53407 / 1.06 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.536 Fit side-chains REVERT: A 88 MET cc_start: 0.8376 (ptp) cc_final: 0.8072 (ptt) REVERT: A 111 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8358 (mt) REVERT: A 157 ASP cc_start: 0.8840 (p0) cc_final: 0.8124 (p0) REVERT: A 278 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7494 (mtt90) REVERT: A 337 ARG cc_start: 0.7581 (mmt-90) cc_final: 0.7065 (mmt90) REVERT: B 88 MET cc_start: 0.8620 (ptp) cc_final: 0.8295 (ptt) REVERT: B 157 ASP cc_start: 0.8881 (p0) cc_final: 0.8115 (p0) REVERT: B 278 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7736 (ttm170) REVERT: B 335 MET cc_start: 0.7423 (mtm) cc_final: 0.6265 (mmt) REVERT: B 337 ARG cc_start: 0.7463 (mmt90) cc_final: 0.6799 (mmt-90) REVERT: C 157 ASP cc_start: 0.8881 (p0) cc_final: 0.8155 (p0) REVERT: C 247 GLN cc_start: 0.8427 (pm20) cc_final: 0.7987 (pt0) REVERT: C 252 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7329 (mm-30) REVERT: C 278 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7629 (mtt90) REVERT: C 335 MET cc_start: 0.6582 (mtm) cc_final: 0.5604 (mmt) REVERT: C 337 ARG cc_start: 0.7200 (mmt-90) cc_final: 0.6955 (mmp80) REVERT: D 92 PHE cc_start: 0.8432 (t80) cc_final: 0.8149 (t80) REVERT: D 157 ASP cc_start: 0.8866 (p0) cc_final: 0.8138 (p0) REVERT: D 247 GLN cc_start: 0.8445 (pm20) cc_final: 0.7970 (pt0) REVERT: D 337 ARG cc_start: 0.7293 (mmt90) cc_final: 0.6668 (mmt-90) REVERT: E 157 ASP cc_start: 0.8889 (p0) cc_final: 0.8223 (p0) REVERT: E 337 ARG cc_start: 0.7333 (mmt90) cc_final: 0.6654 (mmt-90) outliers start: 41 outliers final: 34 residues processed: 262 average time/residue: 0.1476 time to fit residues: 53.4414 Evaluate side-chains 261 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 144 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.128254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.091106 restraints weight = 15379.654| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.22 r_work: 0.2740 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 14755 Z= 0.240 Angle : 0.614 5.564 19945 Z= 0.324 Chirality : 0.046 0.177 2245 Planarity : 0.005 0.046 2395 Dihedral : 12.774 59.982 2300 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.62 % Allowed : 10.43 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1660 helix: 1.80 (0.23), residues: 580 sheet: 0.38 (0.23), residues: 475 loop : 0.31 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 337 TYR 0.024 0.002 TYR D 272 PHE 0.015 0.002 PHE E 159 TRP 0.011 0.002 TRP E 349 HIS 0.006 0.002 HIS E 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.24 (14740) covalent geometry : angle 0.61029 / 0.32 (19905) SS BOND : bond 0.00256 / 0.14 ( 5) SS BOND : angle 1.32369 / 0.75 ( 10) hydrogen bonds : bond 0.07423 / 4.89 ( 715) hydrogen bonds : angle 4.12780 / 2.84 ( 2145) link_NAG-ASN : bond 0.00395 / 0.26 ( 10) link_NAG-ASN : angle 1.62373 / 1.12 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 0.501 Fit side-chains REVERT: A 88 MET cc_start: 0.8327 (ptp) cc_final: 0.8008 (ptt) REVERT: A 337 ARG cc_start: 0.7583 (mmt-90) cc_final: 0.7033 (mmt90) REVERT: B 88 MET cc_start: 0.8535 (ptp) cc_final: 0.8218 (ptt) REVERT: B 106 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: B 157 ASP cc_start: 0.8931 (p0) cc_final: 0.8658 (p0) REVERT: B 278 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7720 (ttm170) REVERT: B 335 MET cc_start: 0.7553 (mtm) cc_final: 0.7277 (mtp) REVERT: B 337 ARG cc_start: 0.7444 (mmt90) cc_final: 0.6709 (mmt-90) REVERT: C 247 GLN cc_start: 0.8393 (pm20) cc_final: 0.7930 (pt0) REVERT: C 252 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7370 (mm-30) REVERT: C 278 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7585 (mtt90) REVERT: C 335 MET cc_start: 0.6923 (mtm) cc_final: 0.5907 (mmt) REVERT: D 157 ASP cc_start: 0.8931 (p0) cc_final: 0.8634 (p0) REVERT: D 247 GLN cc_start: 0.8444 (pm20) cc_final: 0.7956 (pt0) REVERT: D 337 ARG cc_start: 0.7306 (mmt90) cc_final: 0.6586 (mmt-90) REVERT: E 157 ASP cc_start: 0.8928 (p0) cc_final: 0.8279 (p0) outliers start: 40 outliers final: 35 residues processed: 258 average time/residue: 0.1531 time to fit residues: 54.0475 Evaluate side-chains 262 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 140 optimal weight: 0.8980 chunk 162 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.132758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.095794 restraints weight = 15106.245| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.22 r_work: 0.2804 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14755 Z= 0.117 Angle : 0.474 5.246 19945 Z= 0.254 Chirality : 0.041 0.158 2245 Planarity : 0.004 0.050 2395 Dihedral : 11.975 59.445 2300 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.84 % Allowed : 11.28 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.59 (0.22), residues: 1660 helix: 2.08 (0.23), residues: 580 sheet: 0.73 (0.26), residues: 420 loop : 0.49 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 337 TYR 0.021 0.002 TYR D 272 PHE 0.011 0.001 PHE E 356 TRP 0.015 0.001 TRP E 349 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (14740) covalent geometry : angle 0.47149 / 0.25 (19905) SS BOND : bond 0.00141 / 0.08 ( 5) SS BOND : angle 0.52195 / 0.30 ( 10) hydrogen bonds : bond 0.05494 / 3.61 ( 715) hydrogen bonds : angle 3.76614 / 2.59 ( 2145) link_NAG-ASN : bond 0.00391 / 0.26 ( 10) link_NAG-ASN : angle 1.26308 / 0.88 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.540 Fit side-chains REVERT: A 88 MET cc_start: 0.8342 (ptp) cc_final: 0.8013 (ptt) REVERT: A 111 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8275 (mt) REVERT: A 157 ASP cc_start: 0.8793 (p0) cc_final: 0.8477 (p0) REVERT: A 278 ARG cc_start: 0.8017 (mtm-85) cc_final: 0.7766 (mtt90) REVERT: A 337 ARG cc_start: 0.7521 (mmt-90) cc_final: 0.6955 (mmt90) REVERT: B 88 MET cc_start: 0.8523 (ptp) cc_final: 0.8201 (ptt) REVERT: B 106 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: B 157 ASP cc_start: 0.8819 (p0) cc_final: 0.8378 (p0) REVERT: B 278 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7654 (ttm170) REVERT: B 335 MET cc_start: 0.7272 (mtm) cc_final: 0.6032 (mmt) REVERT: B 337 ARG cc_start: 0.7422 (mmt90) cc_final: 0.6694 (mmt-90) REVERT: C 157 ASP cc_start: 0.8833 (p0) cc_final: 0.8564 (p0) REVERT: C 247 GLN cc_start: 0.8377 (pm20) cc_final: 0.7911 (pt0) REVERT: C 252 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7297 (mm-30) REVERT: C 278 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7500 (mtt90) REVERT: C 335 MET cc_start: 0.6223 (mtm) cc_final: 0.5891 (mmt) REVERT: D 157 ASP cc_start: 0.8838 (p0) cc_final: 0.8487 (p0) REVERT: D 247 GLN cc_start: 0.8429 (pm20) cc_final: 0.7924 (pt0) REVERT: D 337 ARG cc_start: 0.7265 (mmt90) cc_final: 0.6574 (mmt-90) REVERT: E 337 ARG cc_start: 0.7328 (mmt90) cc_final: 0.6548 (mmt-90) outliers start: 28 outliers final: 24 residues processed: 251 average time/residue: 0.1470 time to fit residues: 51.1859 Evaluate side-chains 258 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.132699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.095670 restraints weight = 15083.954| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.21 r_work: 0.2762 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14755 Z= 0.128 Angle : 0.483 5.248 19945 Z= 0.257 Chirality : 0.041 0.158 2245 Planarity : 0.004 0.036 2395 Dihedral : 11.468 59.903 2300 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.10 % Allowed : 11.28 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.70 (0.22), residues: 1660 helix: 2.16 (0.23), residues: 580 sheet: 0.80 (0.26), residues: 420 loop : 0.53 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 148 TYR 0.021 0.002 TYR D 272 PHE 0.010 0.001 PHE D 159 TRP 0.012 0.001 TRP A 349 HIS 0.004 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (14740) covalent geometry : angle 0.48130 / 0.26 (19905) SS BOND : bond 0.00178 / 0.10 ( 5) SS BOND : angle 0.71537 / 0.40 ( 10) hydrogen bonds : bond 0.05496 / 3.60 ( 715) hydrogen bonds : angle 3.69128 / 2.53 ( 2145) link_NAG-ASN : bond 0.00379 / 0.25 ( 10) link_NAG-ASN : angle 1.17399 / 0.81 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.447 Fit side-chains REVERT: A 88 MET cc_start: 0.8330 (ptp) cc_final: 0.7994 (ptt) REVERT: A 111 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8239 (mt) REVERT: A 157 ASP cc_start: 0.8825 (p0) cc_final: 0.8391 (p0) REVERT: A 278 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7621 (mtt90) REVERT: A 337 ARG cc_start: 0.7494 (mmt-90) cc_final: 0.6930 (mmt90) REVERT: B 88 MET cc_start: 0.8468 (ptp) cc_final: 0.8137 (ptt) REVERT: B 106 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: B 111 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8171 (mt) REVERT: B 157 ASP cc_start: 0.8859 (p0) cc_final: 0.8421 (p0) REVERT: B 278 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7658 (ttm170) REVERT: B 335 MET cc_start: 0.7219 (mtm) cc_final: 0.6023 (mmt) REVERT: B 337 ARG cc_start: 0.7397 (mmt90) cc_final: 0.6694 (mmt-90) REVERT: C 111 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8334 (mt) REVERT: C 247 GLN cc_start: 0.8381 (pm20) cc_final: 0.7911 (pt0) REVERT: C 252 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7297 (mm-30) REVERT: C 278 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.7543 (mtt90) REVERT: C 335 MET cc_start: 0.6676 (mtm) cc_final: 0.5693 (mmt) REVERT: C 337 ARG cc_start: 0.7330 (mmt90) cc_final: 0.6630 (mmt-90) REVERT: D 157 ASP cc_start: 0.8860 (p0) cc_final: 0.8368 (p0) REVERT: D 247 GLN cc_start: 0.8409 (pm20) cc_final: 0.7912 (pt0) REVERT: D 337 ARG cc_start: 0.7317 (mmt90) cc_final: 0.6585 (mmt-90) REVERT: E 337 ARG cc_start: 0.7355 (mmt90) cc_final: 0.6551 (mmt-90) outliers start: 32 outliers final: 26 residues processed: 247 average time/residue: 0.1464 time to fit residues: 49.7327 Evaluate side-chains 255 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 75 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.135153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.099705 restraints weight = 14979.799| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.01 r_work: 0.2860 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14755 Z= 0.122 Angle : 0.469 5.270 19945 Z= 0.250 Chirality : 0.041 0.157 2245 Planarity : 0.004 0.036 2395 Dihedral : 11.132 59.387 2300 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.10 % Allowed : 11.48 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.76 (0.22), residues: 1660 helix: 2.18 (0.23), residues: 580 sheet: 0.86 (0.27), residues: 420 loop : 0.58 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 148 TYR 0.020 0.002 TYR D 272 PHE 0.010 0.001 PHE E 356 TRP 0.013 0.001 TRP A 349 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (14740) covalent geometry : angle 0.46717 / 0.25 (19905) SS BOND : bond 0.00169 / 0.09 ( 5) SS BOND : angle 0.65411 / 0.37 ( 10) hydrogen bonds : bond 0.05263 / 3.45 ( 715) hydrogen bonds : angle 3.62330 / 2.48 ( 2145) link_NAG-ASN : bond 0.00403 / 0.27 ( 10) link_NAG-ASN : angle 1.08388 / 0.74 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.471 Fit side-chains REVERT: A 88 MET cc_start: 0.8393 (ptp) cc_final: 0.8076 (ptt) REVERT: A 111 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8348 (mt) REVERT: A 157 ASP cc_start: 0.8798 (p0) cc_final: 0.8352 (p0) REVERT: A 278 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7772 (mtt90) REVERT: A 337 ARG cc_start: 0.7456 (mmt-90) cc_final: 0.6948 (mmt90) REVERT: B 88 MET cc_start: 0.8552 (ptp) cc_final: 0.8240 (ptt) REVERT: B 106 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: B 111 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8322 (mt) REVERT: B 157 ASP cc_start: 0.8795 (p0) cc_final: 0.8349 (p0) REVERT: B 278 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7740 (ttm170) REVERT: B 335 MET cc_start: 0.7316 (mtm) cc_final: 0.6217 (mmt) REVERT: B 337 ARG cc_start: 0.7361 (mmt90) cc_final: 0.6738 (mmt-90) REVERT: C 111 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8446 (mt) REVERT: C 157 ASP cc_start: 0.8821 (p0) cc_final: 0.8545 (p0) REVERT: C 247 GLN cc_start: 0.8474 (pm20) cc_final: 0.7978 (pt0) REVERT: C 252 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7401 (mm-30) REVERT: C 278 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7644 (mtt90) REVERT: C 335 MET cc_start: 0.6980 (mtm) cc_final: 0.6008 (mmt) REVERT: C 337 ARG cc_start: 0.7378 (mmt90) cc_final: 0.6729 (mmt-90) REVERT: D 157 ASP cc_start: 0.8814 (p0) cc_final: 0.8450 (p0) REVERT: D 247 GLN cc_start: 0.8464 (pm20) cc_final: 0.7958 (pt0) REVERT: D 337 ARG cc_start: 0.7320 (mmt90) cc_final: 0.6629 (mmt-90) REVERT: E 337 ARG cc_start: 0.7331 (mmt90) cc_final: 0.6621 (mmt-90) outliers start: 32 outliers final: 27 residues processed: 251 average time/residue: 0.1568 time to fit residues: 54.5780 Evaluate side-chains 260 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 105 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.132843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.097444 restraints weight = 14998.346| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.00 r_work: 0.2785 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14755 Z= 0.162 Angle : 0.515 5.232 19945 Z= 0.274 Chirality : 0.042 0.160 2245 Planarity : 0.004 0.036 2395 Dihedral : 11.232 59.838 2300 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.10 % Allowed : 11.34 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.22), residues: 1660 helix: 2.11 (0.23), residues: 580 sheet: 0.70 (0.26), residues: 420 loop : 0.45 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.023 0.002 TYR D 272 PHE 0.012 0.001 PHE D 159 TRP 0.009 0.001 TRP E 230 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (14740) covalent geometry : angle 0.51318 / 0.27 (19905) SS BOND : bond 0.00188 / 0.10 ( 5) SS BOND : angle 0.91628 / 0.52 ( 10) hydrogen bonds : bond 0.06062 / 3.98 ( 715) hydrogen bonds : angle 3.75578 / 2.57 ( 2145) link_NAG-ASN : bond 0.00365 / 0.24 ( 10) link_NAG-ASN : angle 1.10033 / 0.74 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.564 Fit side-chains REVERT: A 88 MET cc_start: 0.8408 (ptp) cc_final: 0.8099 (ptt) REVERT: A 111 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8345 (mt) REVERT: A 278 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7748 (mtt90) REVERT: A 337 ARG cc_start: 0.7495 (mmt-90) cc_final: 0.6991 (mmt90) REVERT: B 88 MET cc_start: 0.8555 (ptp) cc_final: 0.8258 (ptt) REVERT: B 106 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: B 111 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8306 (mt) REVERT: B 157 ASP cc_start: 0.8882 (p0) cc_final: 0.8104 (p0) REVERT: B 278 ARG cc_start: 0.8013 (mtm-85) cc_final: 0.7723 (ttm170) REVERT: B 335 MET cc_start: 0.7440 (mtm) cc_final: 0.6307 (mmt) REVERT: B 337 ARG cc_start: 0.7381 (mmt90) cc_final: 0.6743 (mmt-90) REVERT: C 111 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8444 (mt) REVERT: C 185 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8297 (mttp) REVERT: C 247 GLN cc_start: 0.8494 (pm20) cc_final: 0.7999 (pt0) REVERT: C 252 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7427 (mm-30) REVERT: C 278 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7662 (mtt90) REVERT: C 335 MET cc_start: 0.7192 (mtm) cc_final: 0.6376 (mmt) REVERT: D 157 ASP cc_start: 0.8870 (p0) cc_final: 0.8098 (p0) REVERT: D 247 GLN cc_start: 0.8525 (pm20) cc_final: 0.8003 (pt0) REVERT: D 337 ARG cc_start: 0.7338 (mmt90) cc_final: 0.6627 (mmt-90) REVERT: E 146 ASP cc_start: 0.8215 (p0) cc_final: 0.7810 (p0) REVERT: E 337 ARG cc_start: 0.7333 (mmt90) cc_final: 0.6597 (mmt-90) outliers start: 32 outliers final: 28 residues processed: 252 average time/residue: 0.1456 time to fit residues: 50.5023 Evaluate side-chains 264 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 68 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 107 optimal weight: 0.0570 chunk 31 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.137222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.102573 restraints weight = 14845.082| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.96 r_work: 0.2851 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14755 Z= 0.109 Angle : 0.454 5.311 19945 Z= 0.243 Chirality : 0.041 0.156 2245 Planarity : 0.004 0.037 2395 Dihedral : 10.810 59.578 2300 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.16 % Allowed : 11.34 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.81 (0.22), residues: 1660 helix: 2.22 (0.23), residues: 580 sheet: 0.89 (0.27), residues: 420 loop : 0.61 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.020 0.002 TYR D 272 PHE 0.010 0.001 PHE E 356 TRP 0.015 0.001 TRP A 349 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (14740) covalent geometry : angle 0.45286 / 0.24 (19905) SS BOND : bond 0.00170 / 0.09 ( 5) SS BOND : angle 0.53975 / 0.31 ( 10) hydrogen bonds : bond 0.05028 / 3.30 ( 715) hydrogen bonds : angle 3.54503 / 2.43 ( 2145) link_NAG-ASN : bond 0.00387 / 0.26 ( 10) link_NAG-ASN : angle 0.99201 / 0.68 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3491.57 seconds wall clock time: 60 minutes 48.09 seconds (3648.09 seconds total)