Starting phenix.real_space_refine on Fri Jun 13 10:43:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oq7_17107/06_2025/8oq7_17107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oq7_17107/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oq7_17107/06_2025/8oq7_17107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oq7_17107/06_2025/8oq7_17107.map" model { file = "/net/cci-nas-00/data/ceres_data/8oq7_17107/06_2025/8oq7_17107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oq7_17107/06_2025/8oq7_17107.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} 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: 10.65, per 1000 atoms: 0.72 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: 3.60 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.49 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: 4.91 Time building geometry restraints manager: 4.19 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: 0.02 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: 5.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.040 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 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:14.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.900 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.003 TRP C 349 HIS 0.008 0.002 HIS D 126 PHE 0.023 0.003 PHE B 356 TYR 0.020 0.003 TYR E 219 ARG 0.008 0.001 ARG D 165 Details of bonding type rmsd link_NAG-ASN : bond 0.05604 ( 10) link_NAG-ASN : angle 27.99127 ( 30) hydrogen bonds : bond 0.20322 ( 695) hydrogen bonds : angle 5.71522 ( 2175) covalent geometry : bond 0.00662 (14530) covalent geometry : angle 0.87386 (19625) *********************** 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 : 1.678 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: 1.5680 time to fit residues: 454.6336 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 : 1.557 ------------------------------------------------------------------------------- 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 139 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3574 r_free = 0.3574 target = 0.144913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.118400 restraints weight = 11441.780| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.03 r_work: 0.3125 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1391 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= 0.205 Angle : 0.620 6.211 19655 Z= 0.346 Chirality : 0.044 0.153 2230 Planarity : 0.004 0.034 2355 Dihedral : 7.122 56.947 2358 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.37 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.20), residues: 1660 helix: 2.62 (0.22), residues: 540 sheet: 1.47 (0.24), residues: 425 loop : 0.85 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 349 HIS 0.006 0.001 HIS D 126 PHE 0.020 0.002 PHE A 356 TYR 0.019 0.002 TYR B 340 ARG 0.002 0.000 ARG E 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 10) link_NAG-ASN : angle 2.35700 ( 30) hydrogen bonds : bond 0.09167 ( 695) hydrogen bonds : angle 4.39574 ( 2175) covalent geometry : bond 0.00316 (14530) covalent geometry : angle 0.61383 (19625) *********************** 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 255 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8726 (mm) cc_final: 0.8175 (tp) REVERT: A 337 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7530 (mtt180) REVERT: B 337 ARG cc_start: 0.7914 (mtt180) cc_final: 0.7689 (mtt-85) REVERT: C 281 ILE cc_start: 0.8736 (mm) cc_final: 0.8185 (tp) REVERT: C 304 TRP cc_start: 0.8469 (m100) cc_final: 0.8264 (m-90) REVERT: D 281 ILE cc_start: 0.8756 (mm) cc_final: 0.8513 (mp) REVERT: E 281 ILE cc_start: 0.8736 (mm) cc_final: 0.8208 (tp) outliers start: 26 outliers final: 6 residues processed: 236 average time/residue: 1.4853 time to fit residues: 380.2010 Evaluate side-chains 225 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 E 287 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.142760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.115885 restraints weight = 11291.381| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.03 r_work: 0.3093 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1522 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= 0.225 Angle : 0.633 5.815 19655 Z= 0.356 Chirality : 0.044 0.162 2230 Planarity : 0.004 0.037 2355 Dihedral : 7.317 58.187 2355 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.46 % Allowed : 6.71 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.20), residues: 1660 helix: 2.59 (0.22), residues: 540 sheet: 1.31 (0.24), residues: 425 loop : 0.69 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 349 HIS 0.008 0.002 HIS B 126 PHE 0.020 0.002 PHE D 356 TYR 0.017 0.002 TYR D 340 ARG 0.002 0.000 ARG B 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 10) link_NAG-ASN : angle 1.89944 ( 30) hydrogen bonds : bond 0.09661 ( 695) hydrogen bonds : angle 4.43143 ( 2175) covalent geometry : bond 0.00350 (14530) covalent geometry : angle 0.62943 (19625) *********************** 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 251 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8790 (mm) cc_final: 0.8243 (tp) REVERT: B 337 ARG cc_start: 0.7935 (mtt180) cc_final: 0.7692 (mtt-85) REVERT: C 281 ILE cc_start: 0.8762 (mm) cc_final: 0.8191 (tp) REVERT: C 304 TRP cc_start: 0.8494 (m100) cc_final: 0.8270 (m-90) REVERT: D 281 ILE cc_start: 0.8771 (mm) cc_final: 0.8519 (mp) REVERT: E 281 ILE cc_start: 0.8790 (mm) cc_final: 0.8241 (tp) outliers start: 37 outliers final: 7 residues processed: 226 average time/residue: 1.4636 time to fit residues: 359.6078 Evaluate side-chains 215 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 208 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain E residue 197 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 C 199 ASN C 251 GLN D 181 GLN D 199 ASN D 251 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 = 0.3469 r_free = 0.3469 target = 0.136619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.113225 restraints weight = 10966.367| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 0.85 r_work: 0.3045 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14540 Z= 0.290 Angle : 0.738 5.923 19655 Z= 0.419 Chirality : 0.048 0.224 2230 Planarity : 0.005 0.042 2355 Dihedral : 8.626 58.492 2355 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.52 % Allowed : 6.91 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 1660 helix: 2.36 (0.21), residues: 540 sheet: 1.23 (0.26), residues: 355 loop : 0.36 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 349 HIS 0.010 0.002 HIS D 126 PHE 0.023 0.002 PHE D 356 TYR 0.018 0.003 TYR D 340 ARG 0.004 0.000 ARG B 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 10) link_NAG-ASN : angle 1.62644 ( 30) hydrogen bonds : bond 0.11273 ( 695) hydrogen bonds : angle 4.64032 ( 2175) covalent geometry : bond 0.00474 (14530) covalent geometry : angle 0.73630 (19625) *********************** 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 254 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8887 (mm) cc_final: 0.8389 (tp) REVERT: B 337 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7695 (mtt-85) REVERT: C 281 ILE cc_start: 0.8869 (mm) cc_final: 0.8364 (tp) REVERT: C 304 TRP cc_start: 0.8548 (m100) cc_final: 0.8307 (m-90) REVERT: D 200 MET cc_start: 0.8670 (mtt) cc_final: 0.8412 (mtp) REVERT: D 281 ILE cc_start: 0.8864 (mm) cc_final: 0.8630 (mp) REVERT: E 281 ILE cc_start: 0.8874 (mm) cc_final: 0.8372 (tp) outliers start: 38 outliers final: 16 residues processed: 229 average time/residue: 1.6188 time to fit residues: 401.7843 Evaluate side-chains 224 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 C residue 122 LEU 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 E residue 122 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 145 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 C 199 ASN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.139378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.116235 restraints weight = 11239.703| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 0.86 r_work: 0.3090 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1720 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= 0.230 Angle : 0.636 5.335 19655 Z= 0.360 Chirality : 0.045 0.169 2230 Planarity : 0.005 0.041 2355 Dihedral : 8.318 58.755 2355 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.59 % Allowed : 7.64 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 1660 helix: 2.50 (0.21), residues: 540 sheet: 1.05 (0.25), residues: 370 loop : 0.37 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 349 HIS 0.008 0.002 HIS C 126 PHE 0.021 0.002 PHE D 356 TYR 0.017 0.002 TYR B 340 ARG 0.003 0.000 ARG C 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 10) link_NAG-ASN : angle 1.09567 ( 30) hydrogen bonds : bond 0.09676 ( 695) hydrogen bonds : angle 4.39174 ( 2175) covalent geometry : bond 0.00359 (14530) covalent geometry : angle 0.63533 (19625) *********************** 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 251 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8849 (mm) cc_final: 0.8352 (tp) REVERT: B 238 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8123 (mptp) REVERT: B 337 ARG cc_start: 0.7881 (mtt180) cc_final: 0.7629 (mtt-85) REVERT: C 281 ILE cc_start: 0.8840 (mm) cc_final: 0.8330 (tp) REVERT: C 304 TRP cc_start: 0.8546 (m100) cc_final: 0.8306 (m-90) REVERT: D 200 MET cc_start: 0.8651 (mtt) cc_final: 0.8391 (mtp) REVERT: D 281 ILE cc_start: 0.8825 (mm) cc_final: 0.8583 (mp) REVERT: E 281 ILE cc_start: 0.8867 (mm) cc_final: 0.8370 (tp) outliers start: 39 outliers final: 13 residues processed: 225 average time/residue: 1.5558 time to fit residues: 379.1276 Evaluate side-chains 222 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 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 122 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 E residue 197 MET Chi-restraints excluded: chain E residue 212 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 135 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 140 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ** 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 = 0.3512 r_free = 0.3512 target = 0.140228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.117148 restraints weight = 11251.188| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 0.86 r_work: 0.3103 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14540 Z= 0.217 Angle : 0.613 5.083 19655 Z= 0.347 Chirality : 0.044 0.162 2230 Planarity : 0.004 0.039 2355 Dihedral : 8.188 59.222 2355 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.66 % Allowed : 8.31 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.20), residues: 1660 helix: 2.59 (0.22), residues: 540 sheet: 1.06 (0.25), residues: 370 loop : 0.39 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 349 HIS 0.007 0.002 HIS A 126 PHE 0.020 0.002 PHE D 356 TYR 0.017 0.002 TYR B 340 ARG 0.002 0.000 ARG B 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 10) link_NAG-ASN : angle 0.85635 ( 30) hydrogen bonds : bond 0.09295 ( 695) hydrogen bonds : angle 4.33310 ( 2175) covalent geometry : bond 0.00336 (14530) covalent geometry : angle 0.61293 (19625) *********************** 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 252 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8833 (mm) cc_final: 0.8331 (tp) REVERT: B 238 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8097 (mptp) REVERT: C 281 ILE cc_start: 0.8821 (mm) cc_final: 0.8309 (tp) REVERT: C 304 TRP cc_start: 0.8541 (m100) cc_final: 0.8304 (m-90) REVERT: D 200 MET cc_start: 0.8651 (mtt) cc_final: 0.8389 (mtp) REVERT: D 281 ILE cc_start: 0.8812 (mm) cc_final: 0.8569 (mp) REVERT: E 281 ILE cc_start: 0.8856 (mm) cc_final: 0.8361 (tp) outliers start: 40 outliers final: 16 residues processed: 231 average time/residue: 1.8966 time to fit residues: 475.7010 Evaluate side-chains 228 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 2.748 ------------------------------------------------------------------------------- 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 177 MET 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 122 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 D residue 310 VAL 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 128 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 153 optimal weight: 4.9990 chunk 138 optimal weight: 0.1980 chunk 107 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.140270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.117181 restraints weight = 11289.873| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 0.86 r_work: 0.3104 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14540 Z= 0.216 Angle : 0.612 5.119 19655 Z= 0.346 Chirality : 0.044 0.161 2230 Planarity : 0.004 0.039 2355 Dihedral : 8.178 59.813 2355 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.72 % Allowed : 8.37 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.20), residues: 1660 helix: 2.59 (0.22), residues: 540 sheet: 1.07 (0.25), residues: 370 loop : 0.39 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 349 HIS 0.007 0.001 HIS A 126 PHE 0.021 0.002 PHE D 356 TYR 0.017 0.002 TYR B 340 ARG 0.002 0.000 ARG B 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 10) link_NAG-ASN : angle 0.82181 ( 30) hydrogen bonds : bond 0.09287 ( 695) hydrogen bonds : angle 4.32846 ( 2175) covalent geometry : bond 0.00335 (14530) covalent geometry : angle 0.61150 (19625) *********************** 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 256 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8827 (mm) cc_final: 0.8325 (tp) REVERT: B 238 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8101 (mptp) REVERT: C 281 ILE cc_start: 0.8826 (mm) cc_final: 0.8311 (tp) REVERT: C 304 TRP cc_start: 0.8541 (m100) cc_final: 0.8302 (m-90) REVERT: D 200 MET cc_start: 0.8638 (mtt) cc_final: 0.8375 (mtp) REVERT: D 281 ILE cc_start: 0.8812 (mm) cc_final: 0.8570 (mp) REVERT: E 281 ILE cc_start: 0.8854 (mm) cc_final: 0.8359 (tp) outliers start: 41 outliers final: 17 residues processed: 232 average time/residue: 1.9364 time to fit residues: 485.5915 Evaluate side-chains 229 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 1.743 ------------------------------------------------------------------------------- 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 177 MET 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 122 LEU 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 D residue 310 VAL Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 212 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 44 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 116 optimal weight: 0.0670 chunk 30 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 107 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.141674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.118747 restraints weight = 11220.419| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.86 r_work: 0.3127 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1867 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= 0.199 Angle : 0.584 5.116 19655 Z= 0.329 Chirality : 0.044 0.158 2230 Planarity : 0.004 0.037 2355 Dihedral : 7.933 59.934 2355 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.20), residues: 1660 helix: 2.65 (0.22), residues: 540 sheet: 1.35 (0.24), residues: 415 loop : 0.52 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 349 HIS 0.006 0.001 HIS A 126 PHE 0.020 0.002 PHE D 356 TYR 0.017 0.002 TYR B 340 ARG 0.002 0.000 ARG B 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 10) link_NAG-ASN : angle 0.78347 ( 30) hydrogen bonds : bond 0.08715 ( 695) hydrogen bonds : angle 4.23783 ( 2175) covalent geometry : bond 0.00305 (14530) covalent geometry : angle 0.58412 (19625) *********************** 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 247 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8829 (mm) cc_final: 0.8325 (tp) REVERT: B 238 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8094 (mptp) REVERT: C 281 ILE cc_start: 0.8796 (mm) cc_final: 0.8297 (tp) REVERT: C 304 TRP cc_start: 0.8536 (m100) cc_final: 0.8299 (m-90) REVERT: D 200 MET cc_start: 0.8636 (mtt) cc_final: 0.8372 (mtp) REVERT: D 281 ILE cc_start: 0.8793 (mm) cc_final: 0.8552 (mp) REVERT: E 281 ILE cc_start: 0.8839 (mm) cc_final: 0.8335 (tp) outliers start: 34 outliers final: 16 residues processed: 230 average time/residue: 1.5604 time to fit residues: 390.6050 Evaluate side-chains 228 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 177 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 122 LEU 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 310 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 69 optimal weight: 0.0970 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.141613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.118213 restraints weight = 11157.289| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 0.86 r_work: 0.3116 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14540 Z= 0.217 Angle : 0.614 5.182 19655 Z= 0.347 Chirality : 0.044 0.159 2230 Planarity : 0.004 0.038 2355 Dihedral : 8.044 59.115 2355 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.06 % Allowed : 9.50 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.20), residues: 1660 helix: 2.59 (0.21), residues: 540 sheet: 1.07 (0.25), residues: 370 loop : 0.38 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 349 HIS 0.007 0.001 HIS B 126 PHE 0.021 0.002 PHE D 356 TYR 0.017 0.002 TYR B 340 ARG 0.002 0.000 ARG B 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 10) link_NAG-ASN : angle 0.76132 ( 30) hydrogen bonds : bond 0.09287 ( 695) hydrogen bonds : angle 4.32155 ( 2175) covalent geometry : bond 0.00337 (14530) covalent geometry : angle 0.61334 (19625) *********************** 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: 31 poor density : 209 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8831 (mm) cc_final: 0.8329 (tp) REVERT: B 238 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8109 (mptp) REVERT: C 281 ILE cc_start: 0.8799 (mm) cc_final: 0.8280 (tp) REVERT: C 304 TRP cc_start: 0.8534 (m100) cc_final: 0.8296 (m-90) REVERT: D 200 MET cc_start: 0.8663 (mtt) cc_final: 0.8384 (mtp) REVERT: D 281 ILE cc_start: 0.8800 (mm) cc_final: 0.8556 (mp) REVERT: E 281 ILE cc_start: 0.8831 (mm) cc_final: 0.8326 (tp) outliers start: 31 outliers final: 16 residues processed: 222 average time/residue: 1.5389 time to fit residues: 370.4138 Evaluate side-chains 226 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 177 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 122 LEU 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 310 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 5 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.142829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.119560 restraints weight = 11244.132| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 0.86 r_work: 0.3135 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1906 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= 0.199 Angle : 0.587 5.383 19655 Z= 0.330 Chirality : 0.044 0.157 2230 Planarity : 0.004 0.037 2355 Dihedral : 7.811 58.903 2355 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.66 % Allowed : 10.03 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.20), residues: 1660 helix: 2.63 (0.22), residues: 540 sheet: 1.35 (0.24), residues: 415 loop : 0.52 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 349 HIS 0.006 0.001 HIS A 126 PHE 0.020 0.002 PHE D 356 TYR 0.017 0.002 TYR B 340 ARG 0.002 0.000 ARG B 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 10) link_NAG-ASN : angle 0.75653 ( 30) hydrogen bonds : bond 0.08730 ( 695) hydrogen bonds : angle 4.23390 ( 2175) covalent geometry : bond 0.00307 (14530) covalent geometry : angle 0.58636 (19625) ********************** 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 237 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8823 (mm) cc_final: 0.8321 (tp) REVERT: B 238 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8093 (mptp) REVERT: C 281 ILE cc_start: 0.8769 (mm) cc_final: 0.8262 (tp) REVERT: C 304 TRP cc_start: 0.8531 (m100) cc_final: 0.8290 (m-90) REVERT: D 200 MET cc_start: 0.8652 (mtt) cc_final: 0.8362 (mtp) REVERT: D 281 ILE cc_start: 0.8783 (mm) cc_final: 0.8540 (mp) REVERT: E 281 ILE cc_start: 0.8813 (mm) cc_final: 0.8308 (tp) outliers start: 25 outliers final: 16 residues processed: 225 average time/residue: 1.4682 time to fit residues: 358.9757 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 : 1.565 ------------------------------------------------------------------------------- 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 177 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 122 LEU 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 310 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 116 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.144556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.121950 restraints weight = 11389.074| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 0.85 r_work: 0.3164 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1983 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= 0.178 Angle : 0.554 5.529 19655 Z= 0.311 Chirality : 0.043 0.153 2230 Planarity : 0.004 0.036 2355 Dihedral : 7.413 59.818 2355 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.53 % Allowed : 10.30 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.20), residues: 1660 helix: 2.71 (0.22), residues: 540 sheet: 1.17 (0.24), residues: 425 loop : 0.69 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 349 HIS 0.005 0.001 HIS B 126 PHE 0.020 0.001 PHE D 356 TYR 0.017 0.002 TYR B 340 ARG 0.002 0.000 ARG B 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 10) link_NAG-ASN : angle 0.75755 ( 30) hydrogen bonds : bond 0.08033 ( 695) hydrogen bonds : angle 4.12715 ( 2175) covalent geometry : bond 0.00273 (14530) covalent geometry : angle 0.55413 (19625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13321.03 seconds wall clock time: 230 minutes 7.01 seconds (13807.01 seconds total)