Starting phenix.real_space_refine on Thu Sep 18 06:30:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g78_51115/09_2025/9g78_51115.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g78_51115/09_2025/9g78_51115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g78_51115/09_2025/9g78_51115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g78_51115/09_2025/9g78_51115.map" model { file = "/net/cci-nas-00/data/ceres_data/9g78_51115/09_2025/9g78_51115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g78_51115/09_2025/9g78_51115.cif" } resolution = 3.11 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= 0.001 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 9470 2.51 5 N 2210 2.21 5 O 2515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14270 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2722 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2722 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2722 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2722 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2722 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 150 Unusual residues: {'D10': 2, 'D12': 1, 'HEX': 2, 'NAG': 2, 'OCT': 4, 'P9N': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 127 Unusual residues: {'D10': 2, 'D12': 1, 'HEX': 2, 'NAG': 2, 'OCT': 4, 'P9N': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 127 Unusual residues: {'D10': 2, 'D12': 1, 'HEX': 2, 'NAG': 2, 'OCT': 4, 'P9N': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 127 Unusual residues: {'D10': 2, 'D12': 1, 'HEX': 2, 'NAG': 2, 'OCT': 4, 'P9N': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 104 Unusual residues: {'D10': 2, 'D12': 1, 'HEX': 2, 'NAG': 2, 'OCT': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 4.16, per 1000 atoms: 0.29 Number of scatterers: 14270 At special positions: 0 Unit cell: (96.1675, 95.495, 136.518, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 2515 8.00 N 2210 7.00 C 9470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 502 " - " ASN A 234 " " NAG B 503 " - " ASN B 234 " " NAG C 503 " - " ASN C 234 " " NAG D 503 " - " ASN D 234 " " NAG E 503 " - " ASN E 234 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 722.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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 40.8% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 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: 4.106A 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: 3.775A pdb=" N PHE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.634A pdb=" N TRP A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.526A pdb=" N ILE A 305 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 333 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 342 through 380 removed outlier: 3.515A pdb=" N VAL A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 478 removed outlier: 4.041A 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: 4.106A 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: 3.774A pdb=" N PHE B 284 " --> pdb=" O HIS B 280 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.634A pdb=" N TRP B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.526A pdb=" N ILE B 305 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 333 Proline residue: B 315 - end of helix Processing helix chain 'B' and resid 342 through 380 removed outlier: 3.515A pdb=" N VAL B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 478 removed outlier: 4.041A 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: 4.106A 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: 3.775A pdb=" N PHE C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.634A pdb=" N TRP C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.526A pdb=" N ILE C 305 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 333 Proline residue: C 315 - end of helix Processing helix chain 'C' and resid 342 through 380 removed outlier: 3.515A pdb=" N VAL C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 478 removed outlier: 4.040A 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: 4.106A 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: 3.774A pdb=" N PHE D 284 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.633A pdb=" N TRP D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.526A pdb=" N ILE D 305 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 333 Proline residue: D 315 - end of helix Processing helix chain 'D' and resid 342 through 380 removed outlier: 3.514A pdb=" N VAL D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 478 removed outlier: 4.040A 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: 4.106A 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: 3.775A pdb=" N PHE E 284 " --> pdb=" O HIS E 280 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.634A pdb=" N TRP E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.526A pdb=" N ILE E 305 " --> pdb=" O SER E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 333 Proline residue: E 315 - end of helix Processing helix chain 'E' and resid 342 through 380 removed outlier: 3.514A pdb=" N VAL E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR E 362 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG E 380 " --> pdb=" O GLU E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 478 removed outlier: 4.041A 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: 3.609A pdb=" N TRP A 128 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 removed outlier: 7.030A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE A 168 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG A 191 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 128 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.737A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 210 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER A 218 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN A 269 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR A 276 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU A 252 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ARG A 278 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 5.716A 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: 3.609A pdb=" N TRP B 128 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 168 removed outlier: 7.030A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE B 168 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG B 191 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 128 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.736A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 210 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER B 218 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN B 269 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR B 276 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU B 252 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ARG B 278 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 5.716A 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: 3.610A pdb=" N TRP C 128 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 163 through 168 removed outlier: 7.030A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE C 168 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG C 191 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP C 128 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.737A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 210 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER C 218 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN C 269 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR C 276 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLU C 252 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ARG C 278 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 5.716A 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: 3.609A pdb=" N TRP D 128 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 163 through 168 removed outlier: 7.030A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE D 168 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ARG D 191 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP D 128 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.737A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 210 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER D 218 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN D 269 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR D 276 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU D 252 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ARG D 278 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 5.716A 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: 3.610A pdb=" N TRP E 128 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 163 through 168 removed outlier: 7.029A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE E 168 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG E 191 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP E 128 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.737A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN E 210 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER E 218 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN E 269 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR E 276 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU E 252 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ARG E 278 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE E 250 " --> pdb=" O ARG E 278 " (cutoff:3.500A) 795 hydrogen bonds defined for protein. 2220 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: 2.26 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2625 1.33 - 1.45: 3771 1.45 - 1.57: 8054 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14590 Sorted by residual: bond pdb=" CA VAL D 310 " pdb=" CB VAL D 310 " ideal model delta sigma weight residual 1.539 1.549 -0.010 5.40e-03 3.43e+04 3.65e+00 bond pdb=" CA VAL E 310 " pdb=" CB VAL E 310 " ideal model delta sigma weight residual 1.539 1.549 -0.010 5.40e-03 3.43e+04 3.64e+00 bond pdb=" CA VAL A 310 " pdb=" CB VAL A 310 " ideal model delta sigma weight residual 1.539 1.549 -0.010 5.40e-03 3.43e+04 3.49e+00 bond pdb=" CA VAL B 310 " pdb=" CB VAL B 310 " ideal model delta sigma weight residual 1.539 1.549 -0.010 5.40e-03 3.43e+04 3.11e+00 bond pdb=" CA VAL C 310 " pdb=" CB VAL C 310 " ideal model delta sigma weight residual 1.539 1.548 -0.009 5.40e-03 3.43e+04 2.90e+00 ... (remaining 14585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 18740 1.92 - 3.84: 791 3.84 - 5.76: 164 5.76 - 7.68: 30 7.68 - 9.60: 10 Bond angle restraints: 19735 Sorted by residual: angle pdb=" C ASP A 109 " pdb=" N SER A 110 " pdb=" CA SER A 110 " ideal model delta sigma weight residual 121.80 114.71 7.09 1.71e+00 3.42e-01 1.72e+01 angle pdb=" C ASP D 109 " pdb=" N SER D 110 " pdb=" CA SER D 110 " ideal model delta sigma weight residual 121.80 114.71 7.09 1.71e+00 3.42e-01 1.72e+01 angle pdb=" C ASP B 109 " pdb=" N SER B 110 " pdb=" CA SER B 110 " ideal model delta sigma weight residual 121.80 114.72 7.08 1.71e+00 3.42e-01 1.72e+01 angle pdb=" C ASP E 109 " pdb=" N SER E 110 " pdb=" CA SER E 110 " ideal model delta sigma weight residual 121.80 114.73 7.07 1.71e+00 3.42e-01 1.71e+01 angle pdb=" C ASP C 109 " pdb=" N SER C 110 " pdb=" CA SER C 110 " ideal model delta sigma weight residual 121.80 114.73 7.07 1.71e+00 3.42e-01 1.71e+01 ... (remaining 19730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 8556 16.84 - 33.67: 319 33.67 - 50.51: 35 50.51 - 67.34: 5 67.34 - 84.18: 5 Dihedral angle restraints: 8920 sinusoidal: 3905 harmonic: 5015 Sorted by residual: dihedral pdb=" CA SER D 339 " pdb=" C SER D 339 " pdb=" N TYR D 340 " pdb=" CA TYR D 340 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA SER B 339 " pdb=" C SER B 339 " pdb=" N TYR B 340 " pdb=" CA TYR B 340 " ideal model delta harmonic sigma weight residual 180.00 163.55 16.45 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA SER C 339 " pdb=" C SER C 339 " pdb=" N TYR C 340 " pdb=" CA TYR C 340 " ideal model delta harmonic sigma weight residual 180.00 163.56 16.44 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 8917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 2220 0.163 - 0.325: 35 0.325 - 0.488: 5 0.488 - 0.651: 0 0.651 - 0.814: 5 Chirality restraints: 2265 Sorted by residual: chirality pdb=" C1 NAG D 503 " pdb=" ND2 ASN D 234 " pdb=" C2 NAG D 503 " pdb=" O5 NAG D 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.65e+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 -1.59 -0.81 2.00e-01 2.50e+01 1.65e+01 chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.65e+01 ... (remaining 2262 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " 0.080 2.00e-02 2.50e+03 1.86e-01 4.34e+02 pdb=" CG ASN E 234 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " 0.122 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " -0.344 2.00e-02 2.50e+03 pdb=" C1 NAG E 503 " 0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.080 2.00e-02 2.50e+03 1.86e-01 4.34e+02 pdb=" CG ASN D 234 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " 0.122 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.344 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 B 234 " -0.080 2.00e-02 2.50e+03 1.86e-01 4.34e+02 pdb=" CG ASN B 234 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.122 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " 0.343 2.00e-02 2.50e+03 pdb=" C1 NAG B 503 " -0.181 2.00e-02 2.50e+03 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 95 2.62 - 3.19: 11286 3.19 - 3.76: 19847 3.76 - 4.33: 28492 4.33 - 4.90: 49787 Nonbonded interactions: 109507 Sorted by model distance: nonbonded pdb=" ND2 ASN C 140 " pdb=" C1 NAG C 502 " model vdw 2.055 3.550 nonbonded pdb=" ND2 ASN B 140 " pdb=" C1 NAG B 502 " model vdw 2.055 3.550 nonbonded pdb=" ND2 ASN E 140 " pdb=" C1 NAG E 502 " model vdw 2.055 3.550 nonbonded pdb=" ND2 ASN D 140 " pdb=" C1 NAG D 502 " model vdw 2.055 3.550 nonbonded pdb=" ND2 ASN A 140 " pdb=" C1 NAG A 501 " model vdw 2.055 3.550 ... (remaining 109502 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 504 through 511)) selection = (chain 'B' and (resid 74 through 479 or resid 502 or resid 504 through 511)) selection = (chain 'C' and (resid 74 through 479 or resid 502 or resid 504 through 511)) selection = (chain 'D' and (resid 74 through 479 or resid 502 or resid 504 through 511)) selection = (chain 'E' and (resid 74 through 479 or resid 502 or resid 504 through 511)) } 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: 6.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.940 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.011 0.517 14595 Z= 0.537 Angle : 1.340 41.400 19750 Z= 0.573 Chirality : 0.068 0.814 2265 Planarity : 0.013 0.119 2355 Dihedral : 8.960 84.176 5660 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.34 % Allowed : 2.35 % Favored : 97.32 % 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 aren not related in a simple way. whole: 1.35 (0.20), residues: 1660 helix: 0.97 (0.21), residues: 570 sheet: 1.75 (0.24), residues: 430 loop : 0.39 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.003 ARG E 165 TYR 0.068 0.008 TYR B 188 PHE 0.043 0.006 PHE D 463 TRP 0.033 0.009 TRP D 300 HIS 0.010 0.003 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00525 (14590) covalent geometry : angle 0.95978 (19735) hydrogen bonds : bond 0.20151 ( 705) hydrogen bonds : angle 6.89621 ( 2220) link_NAG-ASN : bond 0.51691 ( 5) link_NAG-ASN : angle 33.93600 ( 15) *********************** 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 334 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 329 time to evaluate : 0.531 Fit side-chains REVERT: A 120 MET cc_start: 0.8817 (ttm) cc_final: 0.8614 (ttp) REVERT: A 225 ASP cc_start: 0.7733 (m-30) cc_final: 0.7275 (m-30) REVERT: A 242 ARG cc_start: 0.7683 (mtp180) cc_final: 0.7242 (mtp180) REVERT: A 337 ARG cc_start: 0.7757 (mtp180) cc_final: 0.7518 (tpp-160) REVERT: A 458 TYR cc_start: 0.8085 (m-80) cc_final: 0.7710 (m-10) REVERT: B 179 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7461 (ttp80) REVERT: B 198 CYS cc_start: 0.8075 (t) cc_final: 0.7622 (p) REVERT: B 225 ASP cc_start: 0.7556 (m-30) cc_final: 0.7132 (m-30) REVERT: B 242 ARG cc_start: 0.7474 (mtp180) cc_final: 0.7020 (mtp-110) REVERT: B 288 THR cc_start: 0.8328 (m) cc_final: 0.7869 (p) REVERT: B 337 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7597 (tpp-160) REVERT: C 288 THR cc_start: 0.8136 (m) cc_final: 0.7605 (p) REVERT: D 179 ARG cc_start: 0.7589 (ttp-170) cc_final: 0.7357 (ttp80) REVERT: D 238 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7589 (mmtm) REVERT: D 242 ARG cc_start: 0.7487 (mtp180) cc_final: 0.7149 (mtm110) REVERT: D 288 THR cc_start: 0.8150 (m) cc_final: 0.7638 (p) REVERT: D 337 ARG cc_start: 0.7721 (mtp180) cc_final: 0.7520 (tpp-160) REVERT: E 225 ASP cc_start: 0.7666 (m-30) cc_final: 0.7309 (m-30) REVERT: E 238 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7646 (mmtm) REVERT: E 242 ARG cc_start: 0.7499 (mtp180) cc_final: 0.7029 (mtp-110) REVERT: E 249 LEU cc_start: 0.8048 (mt) cc_final: 0.7824 (mt) outliers start: 5 outliers final: 3 residues processed: 334 average time/residue: 0.1473 time to fit residues: 68.6137 Evaluate side-chains 212 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 209 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain E residue 344 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 269 ASN B 140 ASN B 269 ASN C 140 ASN C 269 ASN D 140 ASN D 269 ASN D 287 GLN E 140 ASN E 199 ASN E 269 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.105805 restraints weight = 16886.934| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.09 r_work: 0.3095 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14595 Z= 0.127 Angle : 0.530 5.253 19750 Z= 0.278 Chirality : 0.041 0.149 2265 Planarity : 0.004 0.040 2355 Dihedral : 4.753 29.953 2618 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.74 % Allowed : 9.46 % Favored : 88.79 % 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 aren not related in a simple way. whole: 2.11 (0.20), residues: 1660 helix: 2.24 (0.22), residues: 545 sheet: 1.70 (0.25), residues: 430 loop : 0.60 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.019 0.002 TYR C 272 PHE 0.017 0.001 PHE D 356 TRP 0.010 0.001 TRP A 128 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00263 (14590) covalent geometry : angle 0.52747 (19735) hydrogen bonds : bond 0.06113 ( 705) hydrogen bonds : angle 4.33656 ( 2220) link_NAG-ASN : bond 0.00738 ( 5) link_NAG-ASN : angle 2.02069 ( 15) *********************** 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 252 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LYS cc_start: 0.7066 (mmtm) cc_final: 0.6795 (mmtt) REVERT: A 242 ARG cc_start: 0.7747 (mtp180) cc_final: 0.7168 (mtp-110) REVERT: A 288 THR cc_start: 0.7905 (m) cc_final: 0.7514 (p) REVERT: A 337 ARG cc_start: 0.7706 (mtp180) cc_final: 0.7316 (tpp-160) REVERT: B 198 CYS cc_start: 0.7893 (t) cc_final: 0.7112 (p) REVERT: B 242 ARG cc_start: 0.7558 (mtp180) cc_final: 0.6983 (mtp180) REVERT: B 288 THR cc_start: 0.8049 (m) cc_final: 0.7644 (p) REVERT: B 337 ARG cc_start: 0.7750 (mtp180) cc_final: 0.7404 (tpp-160) REVERT: C 102 ASP cc_start: 0.7583 (m-30) cc_final: 0.7335 (m-30) REVERT: C 225 ASP cc_start: 0.7153 (m-30) cc_final: 0.6936 (m-30) REVERT: C 288 THR cc_start: 0.7912 (m) cc_final: 0.7424 (p) REVERT: D 242 ARG cc_start: 0.7526 (mtp180) cc_final: 0.6993 (mtp180) REVERT: D 288 THR cc_start: 0.7964 (m) cc_final: 0.7464 (p) REVERT: D 337 ARG cc_start: 0.7601 (mtp180) cc_final: 0.7315 (tpp-160) REVERT: E 242 ARG cc_start: 0.7575 (mtp180) cc_final: 0.7063 (mtp180) outliers start: 26 outliers final: 21 residues processed: 246 average time/residue: 0.1366 time to fit residues: 48.1173 Evaluate side-chains 226 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 344 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 130 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 96 optimal weight: 0.0980 chunk 32 optimal weight: 0.0010 chunk 152 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN D 199 ASN D 287 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109287 restraints weight = 16822.955| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.05 r_work: 0.3146 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14595 Z= 0.103 Angle : 0.456 5.193 19750 Z= 0.243 Chirality : 0.039 0.139 2265 Planarity : 0.004 0.041 2355 Dihedral : 4.560 31.019 2617 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.74 % Allowed : 10.87 % Favored : 87.38 % 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 aren not related in a simple way. whole: 2.30 (0.21), residues: 1660 helix: 2.62 (0.23), residues: 540 sheet: 1.58 (0.25), residues: 430 loop : 0.68 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.014 0.001 TYR C 272 PHE 0.012 0.001 PHE B 261 TRP 0.008 0.001 TRP C 128 HIS 0.003 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00194 (14590) covalent geometry : angle 0.45500 (19735) hydrogen bonds : bond 0.05096 ( 705) hydrogen bonds : angle 3.92502 ( 2220) link_NAG-ASN : bond 0.00436 ( 5) link_NAG-ASN : angle 1.10664 ( 15) *********************** 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 247 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LYS cc_start: 0.6802 (mmtm) cc_final: 0.6587 (mmtt) REVERT: A 242 ARG cc_start: 0.7741 (mtp180) cc_final: 0.7168 (mtp180) REVERT: A 288 THR cc_start: 0.7818 (m) cc_final: 0.7379 (p) REVERT: A 337 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7352 (tpp-160) REVERT: B 198 CYS cc_start: 0.7891 (t) cc_final: 0.7119 (p) REVERT: B 242 ARG cc_start: 0.7610 (mtp180) cc_final: 0.7036 (mtp180) REVERT: B 251 GLN cc_start: 0.8119 (pm20) cc_final: 0.7660 (pm20) REVERT: B 288 THR cc_start: 0.7983 (m) cc_final: 0.7531 (p) REVERT: B 337 ARG cc_start: 0.7719 (mtp180) cc_final: 0.7400 (tpp-160) REVERT: C 238 LYS cc_start: 0.6719 (mmtm) cc_final: 0.6326 (mmtt) REVERT: C 288 THR cc_start: 0.7861 (m) cc_final: 0.7356 (p) REVERT: C 469 LEU cc_start: 0.7653 (tp) cc_final: 0.7442 (tt) REVERT: D 242 ARG cc_start: 0.7564 (mtp180) cc_final: 0.7059 (mtp180) REVERT: D 288 THR cc_start: 0.7910 (m) cc_final: 0.7381 (p) REVERT: D 337 ARG cc_start: 0.7590 (mtp180) cc_final: 0.7324 (tpp-160) REVERT: E 224 ASP cc_start: 0.7731 (t0) cc_final: 0.7508 (t0) REVERT: E 242 ARG cc_start: 0.7600 (mtp180) cc_final: 0.6560 (ptm160) outliers start: 26 outliers final: 17 residues processed: 236 average time/residue: 0.1265 time to fit residues: 43.2792 Evaluate side-chains 216 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 344 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 158 optimal weight: 0.0000 chunk 6 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 116 optimal weight: 0.0570 overall best weight: 1.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.101777 restraints weight = 16862.045| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.17 r_work: 0.2965 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14595 Z= 0.139 Angle : 0.533 6.250 19750 Z= 0.280 Chirality : 0.041 0.151 2265 Planarity : 0.004 0.045 2355 Dihedral : 5.039 29.774 2617 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.55 % Allowed : 10.34 % Favored : 87.11 % 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 aren not related in a simple way. whole: 1.97 (0.21), residues: 1660 helix: 2.52 (0.23), residues: 540 sheet: 1.25 (0.24), residues: 430 loop : 0.45 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 313 TYR 0.015 0.002 TYR B 123 PHE 0.015 0.002 PHE D 356 TRP 0.009 0.001 TRP A 128 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00306 (14590) covalent geometry : angle 0.53040 (19735) hydrogen bonds : bond 0.06409 ( 705) hydrogen bonds : angle 3.98104 ( 2220) link_NAG-ASN : bond 0.00233 ( 5) link_NAG-ASN : angle 2.08846 ( 15) *********************** 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 245 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LYS cc_start: 0.7139 (mmtm) cc_final: 0.6928 (mmtt) REVERT: A 242 ARG cc_start: 0.7878 (mtp180) cc_final: 0.7233 (mtp180) REVERT: A 288 THR cc_start: 0.8164 (m) cc_final: 0.7790 (p) REVERT: A 337 ARG cc_start: 0.7794 (mtp180) cc_final: 0.7348 (tpp-160) REVERT: B 198 CYS cc_start: 0.8113 (t) cc_final: 0.7355 (p) REVERT: B 242 ARG cc_start: 0.7869 (mtp180) cc_final: 0.6764 (ptm160) REVERT: B 288 THR cc_start: 0.8259 (m) cc_final: 0.7833 (p) REVERT: B 337 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7459 (tpp-160) REVERT: C 102 ASP cc_start: 0.7811 (m-30) cc_final: 0.7611 (m-30) REVERT: C 198 CYS cc_start: 0.8035 (t) cc_final: 0.7207 (p) REVERT: C 224 ASP cc_start: 0.7986 (t0) cc_final: 0.7785 (t0) REVERT: C 238 LYS cc_start: 0.7072 (mmtm) cc_final: 0.6713 (mmtt) REVERT: C 288 THR cc_start: 0.8144 (m) cc_final: 0.7686 (p) REVERT: D 242 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7370 (mtp180) REVERT: D 288 THR cc_start: 0.8203 (m) cc_final: 0.7723 (p) REVERT: D 337 ARG cc_start: 0.7774 (mtp180) cc_final: 0.7408 (tpp-160) REVERT: E 224 ASP cc_start: 0.7896 (t0) cc_final: 0.7619 (t0) REVERT: E 242 ARG cc_start: 0.7807 (mtp180) cc_final: 0.6778 (ptm160) outliers start: 38 outliers final: 28 residues processed: 235 average time/residue: 0.1296 time to fit residues: 44.2543 Evaluate side-chains 228 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.096650 restraints weight = 17071.600| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.15 r_work: 0.3022 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14595 Z= 0.143 Angle : 0.519 5.154 19750 Z= 0.277 Chirality : 0.041 0.153 2265 Planarity : 0.004 0.046 2355 Dihedral : 5.231 28.831 2616 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.75 % Allowed : 11.14 % Favored : 86.11 % 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 aren not related in a simple way. whole: 1.80 (0.20), residues: 1660 helix: 2.43 (0.23), residues: 540 sheet: 1.16 (0.23), residues: 465 loop : 0.23 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 242 TYR 0.016 0.002 TYR E 123 PHE 0.013 0.002 PHE D 356 TRP 0.008 0.001 TRP B 128 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00319 (14590) covalent geometry : angle 0.51796 (19735) hydrogen bonds : bond 0.06608 ( 705) hydrogen bonds : angle 3.99507 ( 2220) link_NAG-ASN : bond 0.00281 ( 5) link_NAG-ASN : angle 1.15974 ( 15) *********************** 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 250 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ARG cc_start: 0.7954 (mtp180) cc_final: 0.6917 (ptm160) REVERT: A 288 THR cc_start: 0.8221 (m) cc_final: 0.7848 (p) REVERT: A 337 ARG cc_start: 0.7851 (mtp180) cc_final: 0.7371 (tpp-160) REVERT: B 88 MET cc_start: 0.7639 (ptp) cc_final: 0.7366 (ptt) REVERT: B 198 CYS cc_start: 0.8209 (t) cc_final: 0.7405 (p) REVERT: B 242 ARG cc_start: 0.7992 (mtp180) cc_final: 0.6875 (ptm160) REVERT: B 287 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.6187 (mp10) REVERT: B 288 THR cc_start: 0.8290 (m) cc_final: 0.7820 (p) REVERT: B 337 ARG cc_start: 0.7879 (mtp180) cc_final: 0.7483 (tpp-160) REVERT: C 102 ASP cc_start: 0.7820 (m-30) cc_final: 0.7605 (m-30) REVERT: C 224 ASP cc_start: 0.7985 (t0) cc_final: 0.7757 (t0) REVERT: C 238 LYS cc_start: 0.7067 (mmtm) cc_final: 0.6714 (mmtt) REVERT: C 288 THR cc_start: 0.8216 (m) cc_final: 0.7758 (p) REVERT: D 242 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7335 (mtp-110) REVERT: D 288 THR cc_start: 0.8266 (m) cc_final: 0.7774 (p) REVERT: D 337 ARG cc_start: 0.7846 (mtp180) cc_final: 0.7505 (tpp-160) REVERT: E 88 MET cc_start: 0.7730 (ptp) cc_final: 0.7501 (ptt) REVERT: E 224 ASP cc_start: 0.7964 (t0) cc_final: 0.7669 (t0) REVERT: E 242 ARG cc_start: 0.7865 (mtp180) cc_final: 0.6847 (ptm160) outliers start: 41 outliers final: 33 residues processed: 236 average time/residue: 0.1299 time to fit residues: 44.4092 Evaluate side-chains 235 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 453 HIS B 453 HIS C 453 HIS D 453 HIS E 287 GLN E 453 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.096498 restraints weight = 17093.870| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.07 r_work: 0.2960 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14595 Z= 0.156 Angle : 0.554 9.263 19750 Z= 0.291 Chirality : 0.042 0.305 2265 Planarity : 0.004 0.048 2355 Dihedral : 5.502 28.788 2616 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.95 % Allowed : 11.48 % Favored : 85.57 % 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 aren not related in a simple way. whole: 1.63 (0.21), residues: 1660 helix: 2.39 (0.23), residues: 540 sheet: 0.99 (0.23), residues: 470 loop : 0.10 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 313 TYR 0.016 0.002 TYR C 123 PHE 0.015 0.002 PHE D 356 TRP 0.010 0.001 TRP B 128 HIS 0.006 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00358 (14590) covalent geometry : angle 0.54569 (19735) hydrogen bonds : bond 0.07009 ( 705) hydrogen bonds : angle 4.02182 ( 2220) link_NAG-ASN : bond 0.00942 ( 5) link_NAG-ASN : angle 3.41081 ( 15) *********************** 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 249 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7904 (tt0) cc_final: 0.7431 (tt0) REVERT: A 242 ARG cc_start: 0.7873 (mtp180) cc_final: 0.7121 (mtp-110) REVERT: A 288 THR cc_start: 0.7934 (m) cc_final: 0.7542 (p) REVERT: A 337 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7206 (tpp-160) REVERT: B 242 ARG cc_start: 0.8008 (mtp180) cc_final: 0.6786 (ptm160) REVERT: B 287 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.5850 (mp10) REVERT: B 288 THR cc_start: 0.7970 (m) cc_final: 0.7458 (p) REVERT: B 337 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7293 (tpp-160) REVERT: C 102 ASP cc_start: 0.7746 (m-30) cc_final: 0.7446 (m-30) REVERT: C 224 ASP cc_start: 0.7985 (t0) cc_final: 0.7740 (t0) REVERT: C 288 THR cc_start: 0.7918 (m) cc_final: 0.7416 (p) REVERT: D 242 ARG cc_start: 0.7816 (mtp180) cc_final: 0.7107 (mtp180) REVERT: D 288 THR cc_start: 0.7967 (m) cc_final: 0.7422 (p) REVERT: D 337 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7239 (tpp-160) REVERT: E 224 ASP cc_start: 0.7977 (t0) cc_final: 0.7654 (t0) REVERT: E 242 ARG cc_start: 0.7702 (mtp180) cc_final: 0.6569 (ptm160) REVERT: E 288 THR cc_start: 0.7884 (m) cc_final: 0.7406 (p) outliers start: 44 outliers final: 35 residues processed: 235 average time/residue: 0.1328 time to fit residues: 45.0116 Evaluate side-chains 230 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 326 THR 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 259 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 137 optimal weight: 3.9990 chunk 134 optimal weight: 0.0970 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 41 optimal weight: 0.0670 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN C 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102632 restraints weight = 16706.185| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.33 r_work: 0.2986 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14595 Z= 0.116 Angle : 0.489 10.219 19750 Z= 0.258 Chirality : 0.040 0.277 2265 Planarity : 0.004 0.046 2355 Dihedral : 5.159 34.597 2616 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.28 % Allowed : 12.62 % Favored : 85.10 % 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 aren not related in a simple way. whole: 1.79 (0.21), residues: 1660 helix: 2.48 (0.23), residues: 540 sheet: 1.23 (0.24), residues: 425 loop : 0.17 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 313 TYR 0.013 0.002 TYR A 340 PHE 0.012 0.001 PHE D 356 TRP 0.009 0.001 TRP C 349 HIS 0.004 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00231 (14590) covalent geometry : angle 0.47928 (19735) hydrogen bonds : bond 0.05799 ( 705) hydrogen bonds : angle 3.83876 ( 2220) link_NAG-ASN : bond 0.00774 ( 5) link_NAG-ASN : angle 3.52480 ( 15) *********************** 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 234 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7300 (mtp-110) REVERT: A 288 THR cc_start: 0.8074 (m) cc_final: 0.7673 (p) REVERT: A 337 ARG cc_start: 0.7897 (mtp180) cc_final: 0.7384 (tpp-160) REVERT: B 242 ARG cc_start: 0.8132 (mtp180) cc_final: 0.6949 (ptm160) REVERT: B 288 THR cc_start: 0.8134 (m) cc_final: 0.7679 (p) REVERT: B 337 ARG cc_start: 0.8004 (mtp180) cc_final: 0.7447 (tpp-160) REVERT: C 224 ASP cc_start: 0.8037 (t0) cc_final: 0.7768 (t0) REVERT: C 287 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.5927 (mp10) REVERT: C 288 THR cc_start: 0.8049 (m) cc_final: 0.7559 (p) REVERT: D 242 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7281 (mtp-110) REVERT: D 288 THR cc_start: 0.8124 (m) cc_final: 0.7602 (p) REVERT: D 337 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7351 (tpp-160) REVERT: E 224 ASP cc_start: 0.8012 (t0) cc_final: 0.7699 (t0) REVERT: E 242 ARG cc_start: 0.7873 (mtp180) cc_final: 0.6815 (ptm160) outliers start: 34 outliers final: 24 residues processed: 224 average time/residue: 0.1265 time to fit residues: 41.2780 Evaluate side-chains 215 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 93 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.100135 restraints weight = 16832.708| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.37 r_work: 0.2953 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14595 Z= 0.141 Angle : 0.523 10.175 19750 Z= 0.276 Chirality : 0.041 0.268 2265 Planarity : 0.004 0.047 2355 Dihedral : 5.326 34.639 2615 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.01 % Allowed : 12.75 % Favored : 85.23 % 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 aren not related in a simple way. whole: 1.70 (0.21), residues: 1660 helix: 2.47 (0.23), residues: 540 sheet: 1.01 (0.23), residues: 475 loop : 0.11 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 374 TYR 0.015 0.002 TYR B 123 PHE 0.014 0.002 PHE D 356 TRP 0.009 0.001 TRP B 128 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00316 (14590) covalent geometry : angle 0.51393 (19735) hydrogen bonds : bond 0.06480 ( 705) hydrogen bonds : angle 3.85848 ( 2220) link_NAG-ASN : bond 0.00748 ( 5) link_NAG-ASN : angle 3.52733 ( 15) *********************** 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 225 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ARG cc_start: 0.8045 (mtp180) cc_final: 0.7299 (mtp-110) REVERT: A 288 THR cc_start: 0.8140 (m) cc_final: 0.7744 (p) REVERT: A 337 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7375 (tpp-160) REVERT: B 242 ARG cc_start: 0.8143 (mtp180) cc_final: 0.6938 (ptm160) REVERT: B 288 THR cc_start: 0.8180 (m) cc_final: 0.7715 (p) REVERT: B 337 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7436 (tpp-160) REVERT: C 224 ASP cc_start: 0.8083 (t0) cc_final: 0.7807 (t0) REVERT: C 287 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.5969 (mp10) REVERT: C 288 THR cc_start: 0.8091 (m) cc_final: 0.7615 (p) REVERT: D 242 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7289 (mtp-110) REVERT: D 288 THR cc_start: 0.8138 (m) cc_final: 0.7619 (p) REVERT: D 337 ARG cc_start: 0.7956 (mtp180) cc_final: 0.7354 (tpp-160) REVERT: E 224 ASP cc_start: 0.8031 (t0) cc_final: 0.7721 (t0) REVERT: E 242 ARG cc_start: 0.7909 (mtp180) cc_final: 0.6815 (ptm160) outliers start: 30 outliers final: 28 residues processed: 216 average time/residue: 0.1334 time to fit residues: 41.7764 Evaluate side-chains 223 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 1 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 0.0040 chunk 88 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.134488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103789 restraints weight = 16858.277| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.39 r_work: 0.3009 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14595 Z= 0.104 Angle : 0.473 10.091 19750 Z= 0.247 Chirality : 0.040 0.279 2265 Planarity : 0.004 0.047 2355 Dihedral : 5.063 35.450 2615 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.88 % Allowed : 12.95 % Favored : 85.17 % 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 aren not related in a simple way. whole: 1.92 (0.21), residues: 1660 helix: 2.58 (0.23), residues: 540 sheet: 1.35 (0.24), residues: 425 loop : 0.22 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 313 TYR 0.014 0.001 TYR C 340 PHE 0.012 0.001 PHE D 356 TRP 0.011 0.001 TRP D 349 HIS 0.003 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00196 (14590) covalent geometry : angle 0.45788 (19735) hydrogen bonds : bond 0.05220 ( 705) hydrogen bonds : angle 3.68825 ( 2220) link_NAG-ASN : bond 0.00923 ( 5) link_NAG-ASN : angle 4.30377 ( 15) *********************** 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 229 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ARG cc_start: 0.8044 (mtp180) cc_final: 0.6913 (ptm160) REVERT: A 288 THR cc_start: 0.8046 (m) cc_final: 0.7644 (p) REVERT: A 337 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7375 (tpp-160) REVERT: B 242 ARG cc_start: 0.8155 (mtp180) cc_final: 0.6962 (ptm160) REVERT: B 288 THR cc_start: 0.8098 (m) cc_final: 0.7638 (p) REVERT: B 337 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7427 (tpp-160) REVERT: C 224 ASP cc_start: 0.8020 (t0) cc_final: 0.7745 (t0) REVERT: C 288 THR cc_start: 0.7996 (m) cc_final: 0.7497 (p) REVERT: D 88 MET cc_start: 0.7671 (ptp) cc_final: 0.7465 (ptt) REVERT: D 242 ARG cc_start: 0.7938 (mtp180) cc_final: 0.7300 (mtp-110) REVERT: D 288 THR cc_start: 0.8083 (m) cc_final: 0.7559 (p) REVERT: D 337 ARG cc_start: 0.7940 (mtp180) cc_final: 0.7339 (tpp-160) REVERT: E 224 ASP cc_start: 0.7999 (t0) cc_final: 0.7696 (t0) REVERT: E 242 ARG cc_start: 0.7908 (mtp180) cc_final: 0.6869 (ptm160) outliers start: 28 outliers final: 24 residues processed: 220 average time/residue: 0.1359 time to fit residues: 43.5563 Evaluate side-chains 218 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.129193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.098410 restraints weight = 16889.056| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.37 r_work: 0.2941 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14595 Z= 0.160 Angle : 0.563 11.063 19750 Z= 0.292 Chirality : 0.043 0.341 2265 Planarity : 0.004 0.047 2355 Dihedral : 5.693 54.520 2615 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.95 % Allowed : 12.89 % Favored : 85.17 % 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 aren not related in a simple way. whole: 1.70 (0.21), residues: 1660 helix: 2.47 (0.23), residues: 540 sheet: 1.14 (0.24), residues: 470 loop : 0.01 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 313 TYR 0.014 0.002 TYR B 123 PHE 0.015 0.002 PHE D 356 TRP 0.010 0.001 TRP A 230 HIS 0.006 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00375 (14590) covalent geometry : angle 0.54597 (19735) hydrogen bonds : bond 0.06778 ( 705) hydrogen bonds : angle 3.84257 ( 2220) link_NAG-ASN : bond 0.01086 ( 5) link_NAG-ASN : angle 5.04536 ( 15) ********************** 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 220 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ARG cc_start: 0.8062 (mtp180) cc_final: 0.6948 (ptm160) REVERT: A 288 THR cc_start: 0.8164 (m) cc_final: 0.7829 (p) REVERT: A 337 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7397 (tpp-160) REVERT: B 242 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7031 (ptm160) REVERT: B 288 THR cc_start: 0.8221 (m) cc_final: 0.7768 (p) REVERT: B 337 ARG cc_start: 0.8023 (mtp180) cc_final: 0.7489 (tpp-160) REVERT: C 102 ASP cc_start: 0.7935 (m-30) cc_final: 0.7730 (m-30) REVERT: C 224 ASP cc_start: 0.8092 (t0) cc_final: 0.7814 (t0) REVERT: C 288 THR cc_start: 0.8141 (m) cc_final: 0.7687 (p) REVERT: D 88 MET cc_start: 0.7727 (ptp) cc_final: 0.7521 (ptt) REVERT: D 242 ARG cc_start: 0.7986 (mtp180) cc_final: 0.6982 (ptm160) REVERT: D 288 THR cc_start: 0.8198 (m) cc_final: 0.7682 (p) REVERT: D 337 ARG cc_start: 0.8000 (mtp180) cc_final: 0.7382 (tpp-160) REVERT: E 224 ASP cc_start: 0.8081 (t0) cc_final: 0.7771 (t0) REVERT: E 242 ARG cc_start: 0.7969 (mtp180) cc_final: 0.6962 (ptm160) outliers start: 29 outliers final: 26 residues processed: 214 average time/residue: 0.1419 time to fit residues: 43.2929 Evaluate side-chains 215 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 150 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.101551 restraints weight = 16725.527| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.34 r_work: 0.2983 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14595 Z= 0.118 Angle : 0.507 12.082 19750 Z= 0.263 Chirality : 0.041 0.313 2265 Planarity : 0.004 0.047 2355 Dihedral : 5.426 52.004 2615 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.68 % Allowed : 13.36 % Favored : 84.97 % 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 aren not related in a simple way. whole: 1.76 (0.21), residues: 1660 helix: 2.49 (0.23), residues: 540 sheet: 1.22 (0.25), residues: 430 loop : 0.11 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 313 TYR 0.014 0.002 TYR C 123 PHE 0.012 0.001 PHE D 356 TRP 0.010 0.001 TRP D 349 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00245 (14590) covalent geometry : angle 0.48801 (19735) hydrogen bonds : bond 0.05784 ( 705) hydrogen bonds : angle 3.72422 ( 2220) link_NAG-ASN : bond 0.00925 ( 5) link_NAG-ASN : angle 4.97500 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3424.24 seconds wall clock time: 59 minutes 30.64 seconds (3570.64 seconds total)