Starting phenix.real_space_refine on Sat Aug 23 21:52:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oq7_17107/08_2025/8oq7_17107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oq7_17107/08_2025/8oq7_17107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oq7_17107/08_2025/8oq7_17107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oq7_17107/08_2025/8oq7_17107.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oq7_17107/08_2025/8oq7_17107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oq7_17107/08_2025/8oq7_17107.map" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 S 75 5.16 5 Cl 2 4.86 5 C 9395 2.51 5 N 2215 2.21 5 O 3010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14702 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2731 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2731 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2731 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2731 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2731 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 109 Unusual residues: {' CL': 1, 'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2, 'OCT': 1, 'VZA': 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: "B" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 109 Unusual residues: {' CL': 1, 'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2, 'OCT': 1, 'VZA': 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: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 108 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2, 'OCT': 1, 'VZA': 1} 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: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 108 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2, 'OCT': 1, 'VZA': 1} 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: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 108 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2, 'OCT': 1, 'VZA': 1} 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: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Time building chain proxies: 3.70, per 1000 atoms: 0.25 Number of scatterers: 14702 At special positions: 0 Unit cell: (94.15, 94.15, 138.535, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 75 16.00 P 5 15.00 O 3010 8.00 N 2215 7.00 C 9395 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 602 " - " ASN A 140 " " NAG A 603 " - " ASN A 234 " " NAG B 503 " - " ASN B 140 " " NAG B 504 " - " ASN B 234 " " NAG C 503 " - " ASN C 140 " " NAG C 504 " - " ASN C 234 " " NAG D 503 " - " ASN D 140 " " NAG D 504 " - " ASN D 234 " " NAG E 503 " - " ASN E 140 " " NAG E 504 " - " ASN E 234 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 630.6 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: 50 helices and 15 sheets defined 42.9% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.730A pdb=" N HIS A 84 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 146 through 153 removed outlier: 3.987A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 153 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 280 through 300 removed outlier: 3.852A pdb=" N PHE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.676A pdb=" N TRP A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 309 through 335 Proline residue: A 315 - end of helix removed outlier: 3.582A pdb=" N SER A 334 " --> pdb=" O GLY A 330 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A 335 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 380 removed outlier: 3.577A pdb=" N VAL A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 478 removed outlier: 4.023A 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 80 through 84 removed outlier: 3.730A pdb=" N HIS B 84 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 146 through 153 removed outlier: 3.987A pdb=" N LYS B 151 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 153 " --> pdb=" O VAL B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 280 through 300 removed outlier: 3.851A pdb=" N PHE B 284 " --> pdb=" O HIS B 280 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.676A pdb=" N TRP B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 309 through 335 Proline residue: B 315 - end of helix removed outlier: 3.581A pdb=" N SER B 334 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 380 removed outlier: 3.577A pdb=" N VAL B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 478 removed outlier: 4.023A 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 80 through 84 removed outlier: 3.730A pdb=" N HIS C 84 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 134 Processing helix chain 'C' and resid 146 through 153 removed outlier: 3.987A pdb=" N LYS C 151 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 153 " --> pdb=" O VAL C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 280 through 300 removed outlier: 3.852A pdb=" N PHE C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.675A pdb=" N TRP C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 309 through 335 Proline residue: C 315 - end of helix removed outlier: 3.582A pdb=" N SER C 334 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 380 removed outlier: 3.577A pdb=" N VAL C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 478 removed outlier: 4.023A 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 80 through 84 removed outlier: 3.730A pdb=" N HIS D 84 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 146 through 153 removed outlier: 3.987A pdb=" N LYS D 151 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE D 153 " --> pdb=" O VAL D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 Processing helix chain 'D' and resid 280 through 300 removed outlier: 3.852A pdb=" N PHE D 284 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.676A pdb=" N TRP D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 309 through 335 Proline residue: D 315 - end of helix removed outlier: 3.582A pdb=" N SER D 334 " --> pdb=" O GLY D 330 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 380 removed outlier: 3.577A pdb=" N VAL D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 478 removed outlier: 4.024A 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 80 through 84 removed outlier: 3.730A pdb=" N HIS E 84 " --> pdb=" O ILE E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 146 through 153 removed outlier: 3.987A pdb=" N LYS E 151 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 153 " --> pdb=" O VAL E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 280 through 300 removed outlier: 3.852A pdb=" N PHE E 284 " --> pdb=" O HIS E 280 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.676A pdb=" N TRP E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 309 through 335 Proline residue: E 315 - end of helix removed outlier: 3.581A pdb=" N SER E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET E 335 " --> pdb=" O VAL E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 380 removed outlier: 3.577A pdb=" N VAL E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR E 362 " --> pdb=" O SER E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 478 removed outlier: 4.023A 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: 7.424A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.352A 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: 6.994A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE A 168 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ARG A 191 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.352A 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: 4.630A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER A 218 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN A 269 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY A 266 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE A 261 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR A 268 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU A 259 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 270 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR A 257 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR A 272 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR A 255 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN A 274 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 253 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 145 removed outlier: 7.423A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.352A 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: 6.993A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE B 168 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ARG B 191 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.352A 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: 4.630A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER B 218 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN B 269 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY B 266 " --> pdb=" O PHE B 261 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE B 261 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR B 268 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 259 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG B 270 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR B 257 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR B 272 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR B 255 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN B 274 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 253 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 143 through 145 removed outlier: 7.424A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.352A 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: 6.994A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE C 168 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ARG C 191 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.352A 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: 4.630A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER C 218 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN C 269 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY C 266 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE C 261 " --> pdb=" O GLY C 266 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR C 268 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU C 259 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG C 270 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR C 257 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TYR C 272 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR C 255 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN C 274 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE C 253 " --> pdb=" O ASN C 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 143 through 145 removed outlier: 7.423A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.352A 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: 6.993A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE D 168 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ARG D 191 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.352A 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: 4.631A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER D 218 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN D 269 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY D 266 " --> pdb=" O PHE D 261 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE D 261 " --> pdb=" O GLY D 266 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR D 268 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU D 259 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG D 270 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR D 257 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TYR D 272 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR D 255 " --> pdb=" O TYR D 272 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN D 274 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE D 253 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 145 removed outlier: 7.424A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.352A 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: 6.994A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE E 168 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ARG E 191 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.352A 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: 4.630A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER E 218 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN E 269 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY E 266 " --> pdb=" O PHE E 261 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE E 261 " --> pdb=" O GLY E 266 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR E 268 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU E 259 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG E 270 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR E 257 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TYR E 272 " --> pdb=" O THR E 255 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR E 255 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN E 274 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE E 253 " --> pdb=" O ASN E 274 " (cutoff:3.500A) 790 hydrogen bonds defined for protein. 2175 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: 2.38 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3762 1.34 - 1.46: 2906 1.46 - 1.58: 7712 1.58 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 14530 Sorted by residual: bond pdb=" C1 VZA E 502 " pdb=" P2 VZA E 502 " ideal model delta sigma weight residual 1.829 1.774 0.055 2.00e-02 2.50e+03 7.68e+00 bond pdb=" C1 VZA C 502 " pdb=" P2 VZA C 502 " ideal model delta sigma weight residual 1.829 1.774 0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" C1 VZA A 601 " pdb=" P2 VZA A 601 " ideal model delta sigma weight residual 1.829 1.774 0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" C1 VZA D 502 " pdb=" P2 VZA D 502 " ideal model delta sigma weight residual 1.829 1.774 0.055 2.00e-02 2.50e+03 7.46e+00 bond pdb=" C1 VZA B 502 " pdb=" P2 VZA B 502 " ideal model delta sigma weight residual 1.829 1.775 0.054 2.00e-02 2.50e+03 7.33e+00 ... (remaining 14525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 17855 1.33 - 2.65: 1295 2.65 - 3.98: 353 3.98 - 5.30: 106 5.30 - 6.63: 16 Bond angle restraints: 19625 Sorted by residual: angle pdb=" N ASP C 157 " pdb=" CA ASP C 157 " pdb=" C ASP C 157 " ideal model delta sigma weight residual 109.11 112.67 -3.56 1.42e+00 4.96e-01 6.28e+00 angle pdb=" N ASP B 157 " pdb=" CA ASP B 157 " pdb=" C ASP B 157 " ideal model delta sigma weight residual 109.11 112.65 -3.54 1.42e+00 4.96e-01 6.21e+00 angle pdb=" N ASP A 157 " pdb=" CA ASP A 157 " pdb=" C ASP A 157 " ideal model delta sigma weight residual 109.11 112.63 -3.52 1.42e+00 4.96e-01 6.15e+00 angle pdb=" N ASP D 157 " pdb=" CA ASP D 157 " pdb=" C ASP D 157 " ideal model delta sigma weight residual 109.11 112.63 -3.52 1.42e+00 4.96e-01 6.14e+00 angle pdb=" N ASP E 157 " pdb=" CA ASP E 157 " pdb=" C ASP E 157 " ideal model delta sigma weight residual 109.11 112.63 -3.52 1.42e+00 4.96e-01 6.14e+00 ... (remaining 19620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 8185 16.12 - 32.24: 410 32.24 - 48.36: 75 48.36 - 64.48: 25 64.48 - 80.60: 10 Dihedral angle restraints: 8705 sinusoidal: 3690 harmonic: 5015 Sorted by residual: dihedral pdb=" CA TYR D 340 " pdb=" C TYR D 340 " pdb=" N ILE D 341 " pdb=" CA ILE D 341 " ideal model delta harmonic sigma weight residual -180.00 -164.72 -15.28 0 5.00e+00 4.00e-02 9.34e+00 dihedral pdb=" CA TYR A 340 " pdb=" C TYR A 340 " pdb=" N ILE A 341 " pdb=" CA ILE A 341 " ideal model delta harmonic sigma weight residual -180.00 -164.72 -15.28 0 5.00e+00 4.00e-02 9.33e+00 dihedral pdb=" CA TYR C 340 " pdb=" C TYR C 340 " pdb=" N ILE C 341 " pdb=" CA ILE C 341 " ideal model delta harmonic sigma weight residual -180.00 -164.76 -15.24 0 5.00e+00 4.00e-02 9.29e+00 ... (remaining 8702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.295: 2220 0.295 - 0.589: 0 0.589 - 0.884: 5 0.884 - 1.179: 0 1.179 - 1.473: 5 Chirality restraints: 2230 Sorted by residual: chirality pdb=" C1 NAG E 504 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 504 " pdb=" O5 NAG E 504 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-01 2.50e+01 5.43e+01 chirality pdb=" C1 NAG C 504 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 504 " pdb=" O5 NAG C 504 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-01 2.50e+01 5.42e+01 chirality pdb=" C1 NAG A 603 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 603 " pdb=" O5 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-01 2.50e+01 5.42e+01 ... (remaining 2227 not shown) Planarity restraints: 2365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " -0.147 2.00e-02 2.50e+03 2.80e-01 9.78e+02 pdb=" CG ASN B 234 " 0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.117 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " 0.499 2.00e-02 2.50e+03 pdb=" C1 NAG B 504 " -0.316 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " -0.147 2.00e-02 2.50e+03 2.80e-01 9.77e+02 pdb=" CG ASN E 234 " 0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " -0.117 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " 0.499 2.00e-02 2.50e+03 pdb=" C1 NAG E 504 " -0.316 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " -0.147 2.00e-02 2.50e+03 2.80e-01 9.77e+02 pdb=" CG ASN D 234 " 0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.117 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " 0.499 2.00e-02 2.50e+03 pdb=" C1 NAG D 504 " -0.316 2.00e-02 2.50e+03 ... (remaining 2362 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3414 2.81 - 3.33: 12997 3.33 - 3.86: 23703 3.86 - 4.38: 29067 4.38 - 4.90: 48887 Nonbonded interactions: 118068 Sorted by model distance: nonbonded pdb=" O PHE D 86 " pdb=" O HOH D 601 " model vdw 2.290 3.040 nonbonded pdb=" O PHE A 86 " pdb=" O HOH A 701 " model vdw 2.290 3.040 nonbonded pdb=" O PHE B 86 " pdb=" O HOH B 601 " model vdw 2.290 3.040 nonbonded pdb=" O PHE E 86 " pdb=" O HOH E 601 " model vdw 2.291 3.040 nonbonded pdb=" O PHE C 86 " pdb=" O HOH C 601 " model vdw 2.291 3.040 ... (remaining 118063 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 74 through 479 or resid 603 or resid 605 through 606)) selection = (chain 'B' and (resid 74 through 479 or resid 503 or resid 505 through 506)) selection = (chain 'C' and (resid 74 through 479 or resid 503 or resid 505 through 506)) selection = (chain 'D' and (resid 74 through 479 or resid 503 or resid 505 through 506)) selection = (chain 'E' and (resid 74 through 479 or resid 503 or resid 505 through 506)) } 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: 4.980 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.180 Find NCS groups from input model: 0.360 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:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.007 0.072 14540 Z= 0.343 Angle : 1.399 40.583 19655 Z= 0.578 Chirality : 0.092 1.473 2230 Planarity : 0.005 0.038 2355 Dihedral : 10.808 80.605 5445 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.33 % Allowed : 2.33 % Favored : 97.34 % 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: 2.27 (0.20), residues: 1660 helix: 2.31 (0.22), residues: 565 sheet: 1.67 (0.23), residues: 435 loop : 0.77 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 165 TYR 0.020 0.003 TYR E 219 PHE 0.023 0.003 PHE B 356 TRP 0.019 0.003 TRP C 349 HIS 0.008 0.002 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00662 (14530) covalent geometry : angle 0.87386 (19625) hydrogen bonds : bond 0.20322 ( 695) hydrogen bonds : angle 5.71522 ( 2175) link_NAG-ASN : bond 0.05604 ( 10) link_NAG-ASN : angle 27.99127 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 263 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8861 (mm) cc_final: 0.8344 (tp) REVERT: C 249 LEU cc_start: 0.8438 (mt) cc_final: 0.8219 (mm) REVERT: C 281 ILE cc_start: 0.8843 (mm) cc_final: 0.8317 (tp) REVERT: C 304 TRP cc_start: 0.8490 (m100) cc_final: 0.8262 (m-90) REVERT: D 200 MET cc_start: 0.8390 (mtt) cc_final: 0.8156 (mtp) REVERT: D 281 ILE cc_start: 0.8814 (mm) cc_final: 0.8567 (mp) REVERT: E 281 ILE cc_start: 0.8817 (mm) cc_final: 0.8321 (tp) outliers start: 5 outliers final: 3 residues processed: 268 average time/residue: 0.7552 time to fit residues: 218.1111 Evaluate side-chains 230 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 227 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 212 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN B 181 GLN B 199 ASN B 251 GLN C 199 ASN C 251 GLN D 199 ASN D 251 GLN E 181 GLN E 199 ASN E 251 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.144212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.117586 restraints weight = 11475.755| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.03 r_work: 0.3114 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 14540 Z= 0.215 Angle : 0.631 6.514 19655 Z= 0.352 Chirality : 0.044 0.156 2230 Planarity : 0.004 0.034 2355 Dihedral : 7.209 56.844 2358 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.73 % Allowed : 6.38 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.20), residues: 1660 helix: 2.60 (0.22), residues: 540 sheet: 1.48 (0.24), residues: 425 loop : 0.83 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 125 TYR 0.019 0.002 TYR B 340 PHE 0.021 0.002 PHE A 356 TRP 0.017 0.002 TRP D 349 HIS 0.006 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00331 (14530) covalent geometry : angle 0.62362 (19625) hydrogen bonds : bond 0.09454 ( 695) hydrogen bonds : angle 4.44404 ( 2175) link_NAG-ASN : bond 0.00447 ( 10) link_NAG-ASN : angle 2.58798 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8741 (mm) cc_final: 0.8188 (tp) REVERT: A 337 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7526 (mtt180) REVERT: B 337 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7690 (mtt-85) REVERT: C 281 ILE cc_start: 0.8746 (mm) cc_final: 0.8192 (tp) REVERT: C 304 TRP cc_start: 0.8473 (m100) cc_final: 0.8266 (m-90) REVERT: D 281 ILE cc_start: 0.8767 (mm) cc_final: 0.8524 (mp) REVERT: E 281 ILE cc_start: 0.8756 (mm) cc_final: 0.8225 (tp) outliers start: 26 outliers final: 7 residues processed: 235 average time/residue: 0.7015 time to fit residues: 178.2715 Evaluate side-chains 228 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 251 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 105 optimal weight: 0.2980 chunk 113 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 107 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 125 optimal weight: 0.0970 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN B 181 GLN B 199 ASN B 251 GLN C 199 ASN C 251 GLN D 181 GLN D 199 ASN D 251 GLN E 181 GLN E 199 ASN E 251 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.149627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.123806 restraints weight = 11823.098| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.04 r_work: 0.3204 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14540 Z= 0.156 Angle : 0.521 5.195 19655 Z= 0.288 Chirality : 0.041 0.146 2230 Planarity : 0.004 0.032 2355 Dihedral : 6.398 57.555 2355 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.19 % Allowed : 6.91 % Favored : 90.90 % 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: 2.29 (0.20), residues: 1660 helix: 2.74 (0.22), residues: 540 sheet: 1.19 (0.24), residues: 430 loop : 0.87 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 191 TYR 0.016 0.001 TYR A 340 PHE 0.016 0.001 PHE E 356 TRP 0.013 0.001 TRP C 349 HIS 0.003 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00236 (14530) covalent geometry : angle 0.51609 (19625) hydrogen bonds : bond 0.07473 ( 695) hydrogen bonds : angle 4.11696 ( 2175) link_NAG-ASN : bond 0.00281 ( 10) link_NAG-ASN : angle 1.82007 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8671 (mm) cc_final: 0.8133 (tp) REVERT: B 337 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7691 (mtt-85) REVERT: C 281 ILE cc_start: 0.8641 (mm) cc_final: 0.8094 (tp) REVERT: C 304 TRP cc_start: 0.8485 (m100) cc_final: 0.8272 (m-90) REVERT: D 281 ILE cc_start: 0.8673 (mm) cc_final: 0.8097 (tp) REVERT: E 281 ILE cc_start: 0.8660 (mm) cc_final: 0.8127 (tp) outliers start: 33 outliers final: 4 residues processed: 237 average time/residue: 0.6139 time to fit residues: 158.1651 Evaluate side-chains 217 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 213 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain E residue 158 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 141 optimal weight: 0.3980 chunk 117 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN B 181 GLN B 199 ASN B 251 GLN B 287 GLN C 199 ASN C 251 GLN D 181 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN E 181 GLN E 251 GLN E 287 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.142550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.119568 restraints weight = 11323.036| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 0.86 r_work: 0.3138 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 14540 Z= 0.194 Angle : 0.576 6.050 19655 Z= 0.324 Chirality : 0.043 0.219 2230 Planarity : 0.004 0.033 2355 Dihedral : 6.712 58.274 2355 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.66 % Allowed : 6.84 % Favored : 90.50 % 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: 2.31 (0.20), residues: 1660 helix: 2.73 (0.22), residues: 540 sheet: 1.45 (0.24), residues: 415 loop : 0.72 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 313 TYR 0.016 0.002 TYR D 340 PHE 0.018 0.002 PHE B 356 TRP 0.012 0.001 TRP C 349 HIS 0.006 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00296 (14530) covalent geometry : angle 0.57299 (19625) hydrogen bonds : bond 0.08594 ( 695) hydrogen bonds : angle 4.20209 ( 2175) link_NAG-ASN : bond 0.00220 ( 10) link_NAG-ASN : angle 1.64559 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8811 (mm) cc_final: 0.8307 (tp) REVERT: B 337 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7711 (mtt-85) REVERT: C 281 ILE cc_start: 0.8760 (mm) cc_final: 0.8257 (tp) REVERT: D 281 ILE cc_start: 0.8784 (mm) cc_final: 0.8538 (mp) REVERT: E 281 ILE cc_start: 0.8794 (mm) cc_final: 0.8287 (tp) outliers start: 40 outliers final: 11 residues processed: 231 average time/residue: 0.6673 time to fit residues: 166.6239 Evaluate side-chains 225 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN B 181 GLN B 199 ASN B 251 GLN B 287 GLN C 199 ASN C 251 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN E 181 GLN E 251 GLN E 287 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.138860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.115436 restraints weight = 11217.837| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 0.86 r_work: 0.3077 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14540 Z= 0.247 Angle : 0.663 5.426 19655 Z= 0.375 Chirality : 0.046 0.167 2230 Planarity : 0.005 0.038 2355 Dihedral : 7.884 57.808 2355 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.72 % Allowed : 8.04 % Favored : 89.24 % 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: 1.89 (0.19), residues: 1660 helix: 2.56 (0.21), residues: 540 sheet: 1.08 (0.25), residues: 370 loop : 0.45 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 313 TYR 0.017 0.002 TYR D 340 PHE 0.021 0.002 PHE D 356 TRP 0.012 0.002 TRP C 349 HIS 0.009 0.002 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00393 (14530) covalent geometry : angle 0.66167 (19625) hydrogen bonds : bond 0.10192 ( 695) hydrogen bonds : angle 4.44325 ( 2175) link_NAG-ASN : bond 0.00106 ( 10) link_NAG-ASN : angle 1.18472 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8861 (mm) cc_final: 0.8364 (tp) REVERT: B 200 MET cc_start: 0.8756 (mtt) cc_final: 0.8543 (mtp) REVERT: B 337 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7653 (mtt-85) REVERT: C 108 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8787 (mt) REVERT: C 281 ILE cc_start: 0.8840 (mm) cc_final: 0.8332 (tp) REVERT: C 337 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7798 (mtt-85) REVERT: D 200 MET cc_start: 0.8653 (mtt) cc_final: 0.8381 (mtp) REVERT: D 281 ILE cc_start: 0.8834 (mm) cc_final: 0.8589 (mp) REVERT: E 281 ILE cc_start: 0.8864 (mm) cc_final: 0.8368 (tp) outliers start: 41 outliers final: 15 residues processed: 231 average time/residue: 0.6170 time to fit residues: 154.6147 Evaluate side-chains 222 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 161 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 199 ASN B 251 GLN B 287 GLN C 199 ASN C 251 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN E 181 GLN E 199 ASN E 251 GLN E 287 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.139334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.116069 restraints weight = 11141.255| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 0.86 r_work: 0.3087 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 14540 Z= 0.235 Angle : 0.641 5.240 19655 Z= 0.363 Chirality : 0.045 0.165 2230 Planarity : 0.005 0.039 2355 Dihedral : 7.997 59.933 2355 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.26 % Allowed : 9.04 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.19), residues: 1660 helix: 2.56 (0.21), residues: 540 sheet: 1.05 (0.25), residues: 370 loop : 0.42 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 313 TYR 0.017 0.002 TYR D 340 PHE 0.020 0.002 PHE D 356 TRP 0.015 0.002 TRP C 349 HIS 0.008 0.002 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00370 (14530) covalent geometry : angle 0.64043 (19625) hydrogen bonds : bond 0.09848 ( 695) hydrogen bonds : angle 4.40007 ( 2175) link_NAG-ASN : bond 0.00147 ( 10) link_NAG-ASN : angle 0.97818 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8867 (mm) cc_final: 0.8366 (tp) REVERT: B 238 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8152 (mptp) REVERT: B 337 ARG cc_start: 0.7881 (mtt180) cc_final: 0.7620 (mtt-85) REVERT: C 281 ILE cc_start: 0.8839 (mm) cc_final: 0.8328 (tp) REVERT: C 337 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7793 (mtt-85) REVERT: D 200 MET cc_start: 0.8651 (mtt) cc_final: 0.8378 (mtp) REVERT: D 281 ILE cc_start: 0.8825 (mm) cc_final: 0.8582 (mp) REVERT: E 281 ILE cc_start: 0.8869 (mm) cc_final: 0.8372 (tp) outliers start: 34 outliers final: 14 residues processed: 225 average time/residue: 0.7684 time to fit residues: 186.4956 Evaluate side-chains 222 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 212 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 92 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN B 181 GLN B 199 ASN B 251 GLN B 287 GLN C 199 ASN C 251 GLN D 181 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN E 181 GLN E 199 ASN E 251 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.137808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.114380 restraints weight = 11080.373| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 0.86 r_work: 0.3062 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 14540 Z= 0.262 Angle : 0.690 5.881 19655 Z= 0.391 Chirality : 0.046 0.169 2230 Planarity : 0.005 0.039 2355 Dihedral : 8.653 59.871 2355 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.66 % Allowed : 8.70 % Favored : 88.64 % 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: 1.73 (0.19), residues: 1660 helix: 2.44 (0.21), residues: 540 sheet: 1.02 (0.25), residues: 370 loop : 0.33 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 313 TYR 0.017 0.002 TYR B 340 PHE 0.022 0.002 PHE D 356 TRP 0.015 0.002 TRP C 349 HIS 0.009 0.002 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00420 (14530) covalent geometry : angle 0.68923 (19625) hydrogen bonds : bond 0.10611 ( 695) hydrogen bonds : angle 4.51868 ( 2175) link_NAG-ASN : bond 0.00130 ( 10) link_NAG-ASN : angle 0.86819 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8860 (mm) cc_final: 0.8375 (tp) REVERT: B 238 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8183 (mptp) REVERT: C 281 ILE cc_start: 0.8865 (mm) cc_final: 0.8362 (tp) REVERT: C 337 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7783 (mtt-85) REVERT: D 200 MET cc_start: 0.8681 (mtt) cc_final: 0.8408 (mtp) REVERT: D 281 ILE cc_start: 0.8851 (mm) cc_final: 0.8620 (mp) REVERT: E 281 ILE cc_start: 0.8871 (mm) cc_final: 0.8375 (tp) outliers start: 40 outliers final: 16 residues processed: 228 average time/residue: 0.7657 time to fit residues: 188.4219 Evaluate side-chains 227 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 158 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 68 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN B 181 GLN B 199 ASN B 251 GLN B 287 GLN C 199 ASN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN E 181 GLN E 199 ASN E 251 GLN E 287 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.144101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.121053 restraints weight = 11297.287| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 0.86 r_work: 0.3156 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14540 Z= 0.184 Angle : 0.564 5.141 19655 Z= 0.317 Chirality : 0.043 0.162 2230 Planarity : 0.004 0.038 2355 Dihedral : 7.862 59.873 2355 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.59 % Allowed : 9.63 % Favored : 88.77 % 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: 2.06 (0.20), residues: 1660 helix: 2.64 (0.22), residues: 540 sheet: 0.99 (0.24), residues: 435 loop : 0.69 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 191 TYR 0.017 0.002 TYR A 340 PHE 0.019 0.001 PHE D 356 TRP 0.018 0.002 TRP D 349 HIS 0.006 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00281 (14530) covalent geometry : angle 0.56382 (19625) hydrogen bonds : bond 0.08368 ( 695) hydrogen bonds : angle 4.19355 ( 2175) link_NAG-ASN : bond 0.00277 ( 10) link_NAG-ASN : angle 0.80612 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8339 (m-30) cc_final: 0.8129 (m-30) REVERT: A 281 ILE cc_start: 0.8811 (mm) cc_final: 0.8312 (tp) REVERT: B 200 MET cc_start: 0.8754 (mtt) cc_final: 0.8468 (mtp) REVERT: B 238 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8092 (mptp) REVERT: C 281 ILE cc_start: 0.8767 (mm) cc_final: 0.8257 (tp) REVERT: C 337 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7732 (mtt-85) REVERT: D 200 MET cc_start: 0.8645 (mtt) cc_final: 0.8378 (mtp) REVERT: D 281 ILE cc_start: 0.8775 (mm) cc_final: 0.8535 (mp) REVERT: E 281 ILE cc_start: 0.8793 (mm) cc_final: 0.8293 (tp) outliers start: 24 outliers final: 12 residues processed: 227 average time/residue: 0.7633 time to fit residues: 187.0363 Evaluate side-chains 224 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN B 199 ASN B 251 GLN B 287 GLN C 199 ASN C 251 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN E 199 ASN E 251 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.142325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.118883 restraints weight = 11244.031| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.87 r_work: 0.3128 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 0.021 14540 Z= 0.207 Angle : 0.597 5.203 19655 Z= 0.337 Chirality : 0.044 0.158 2230 Planarity : 0.004 0.038 2355 Dihedral : 7.893 59.546 2355 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.86 % Allowed : 9.90 % Favored : 88.24 % 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: 1.90 (0.20), residues: 1660 helix: 2.61 (0.21), residues: 540 sheet: 1.08 (0.25), residues: 370 loop : 0.44 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 313 TYR 0.017 0.002 TYR B 340 PHE 0.020 0.002 PHE D 356 TRP 0.015 0.002 TRP C 349 HIS 0.007 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00320 (14530) covalent geometry : angle 0.59686 (19625) hydrogen bonds : bond 0.09002 ( 695) hydrogen bonds : angle 4.26690 ( 2175) link_NAG-ASN : bond 0.00220 ( 10) link_NAG-ASN : angle 0.78998 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8377 (m-30) cc_final: 0.8150 (m-30) REVERT: A 281 ILE cc_start: 0.8825 (mm) cc_final: 0.8320 (tp) REVERT: B 238 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8100 (mptp) REVERT: C 281 ILE cc_start: 0.8789 (mm) cc_final: 0.8277 (tp) REVERT: C 337 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7768 (mtt-85) REVERT: D 200 MET cc_start: 0.8655 (mtt) cc_final: 0.8392 (mtp) REVERT: D 281 ILE cc_start: 0.8798 (mm) cc_final: 0.8557 (mp) REVERT: E 227 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8224 (ttp) REVERT: E 281 ILE cc_start: 0.8815 (mm) cc_final: 0.8307 (tp) outliers start: 28 outliers final: 12 residues processed: 224 average time/residue: 0.7931 time to fit residues: 191.6514 Evaluate side-chains 226 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN B 199 ASN B 251 GLN B 287 GLN C 199 ASN C 251 GLN D 181 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN E 199 ASN E 251 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.139480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.115760 restraints weight = 11077.102| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 0.87 r_work: 0.3081 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 14540 Z= 0.258 Angle : 0.681 5.629 19655 Z= 0.386 Chirality : 0.046 0.168 2230 Planarity : 0.005 0.038 2355 Dihedral : 8.466 59.649 2355 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.46 % Allowed : 10.17 % Favored : 88.37 % 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: 1.74 (0.19), residues: 1660 helix: 2.46 (0.21), residues: 540 sheet: 1.05 (0.25), residues: 370 loop : 0.32 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 313 TYR 0.017 0.002 TYR D 340 PHE 0.021 0.002 PHE D 356 TRP 0.013 0.002 TRP D 349 HIS 0.009 0.002 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00414 (14530) covalent geometry : angle 0.68089 (19625) hydrogen bonds : bond 0.10435 ( 695) hydrogen bonds : angle 4.48586 ( 2175) link_NAG-ASN : bond 0.00134 ( 10) link_NAG-ASN : angle 0.79246 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8864 (mm) cc_final: 0.8359 (tp) REVERT: B 200 MET cc_start: 0.8777 (mtt) cc_final: 0.8562 (mtp) REVERT: B 207 LEU cc_start: 0.8833 (mp) cc_final: 0.8573 (mm) REVERT: B 238 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8168 (mptp) REVERT: C 281 ILE cc_start: 0.8849 (mm) cc_final: 0.8343 (tp) REVERT: C 337 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7743 (mtt-85) REVERT: D 200 MET cc_start: 0.8669 (mtt) cc_final: 0.8405 (mtp) REVERT: D 281 ILE cc_start: 0.8833 (mm) cc_final: 0.8602 (mp) REVERT: E 227 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8241 (ttp) REVERT: E 281 ILE cc_start: 0.8849 (mm) cc_final: 0.8351 (tp) outliers start: 22 outliers final: 12 residues processed: 222 average time/residue: 0.8209 time to fit residues: 196.3028 Evaluate side-chains 224 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 251 GLN B 287 GLN C 199 ASN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN E 181 GLN E 199 ASN E 251 GLN E 287 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.138937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.115692 restraints weight = 11081.435| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 0.88 r_work: 0.3076 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 14540 Z= 0.281 Angle : 0.722 6.243 19655 Z= 0.409 Chirality : 0.048 0.171 2230 Planarity : 0.005 0.038 2355 Dihedral : 9.002 59.824 2355 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.53 % Allowed : 10.23 % Favored : 88.24 % 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: 1.68 (0.19), residues: 1660 helix: 2.32 (0.21), residues: 540 sheet: 1.22 (0.26), residues: 355 loop : 0.26 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 313 TYR 0.017 0.002 TYR B 340 PHE 0.022 0.002 PHE D 356 TRP 0.013 0.002 TRP C 349 HIS 0.010 0.002 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00457 (14530) covalent geometry : angle 0.72143 (19625) hydrogen bonds : bond 0.11057 ( 695) hydrogen bonds : angle 4.60127 ( 2175) link_NAG-ASN : bond 0.00103 ( 10) link_NAG-ASN : angle 0.84090 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6036.52 seconds wall clock time: 103 minutes 28.93 seconds (6208.93 seconds total)