Starting phenix.real_space_refine on Fri May 16 22:08:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oq7_17107/05_2025/8oq7_17107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oq7_17107/05_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_17107/05_2025/8oq7_17107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oq7_17107/05_2025/8oq7_17107.map" model { file = "/net/cci-nas-00/data/ceres_data/8oq7_17107/05_2025/8oq7_17107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oq7_17107/05_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-5687/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: 9.61, per 1000 atoms: 0.65 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: 3.61 Conformation dependent library (CDL) restraints added in 1.7 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: 4.58 Time building geometry restraints manager: 4.15 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: 8.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.460 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.840 ------------------------------------------------------------------------------- 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 : 1.523 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: 1.4962 time to fit residues: 433.5378 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 : 1.515 ------------------------------------------------------------------------------- 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 = 0.118401 restraints weight = 11441.779| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.03 r_work: 0.3127 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- 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 2.35699 ( 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 : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8727 (mm) cc_final: 0.8178 (tp) REVERT: A 337 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7523 (mtt180) REVERT: B 337 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7689 (mtt-85) REVERT: C 281 ILE cc_start: 0.8738 (mm) cc_final: 0.8189 (tp) REVERT: C 304 TRP cc_start: 0.8478 (m100) cc_final: 0.8277 (m-90) REVERT: D 281 ILE cc_start: 0.8757 (mm) cc_final: 0.8515 (mp) REVERT: E 281 ILE cc_start: 0.8739 (mm) cc_final: 0.8212 (tp) outliers start: 26 outliers final: 6 residues processed: 236 average time/residue: 1.4566 time to fit residues: 372.7527 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 : 1.504 ------------------------------------------------------------------------------- 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: 0.1980 chunk 161 optimal weight: 0.3980 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 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: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.146456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120175 restraints weight = 11490.289| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.03 r_work: 0.3154 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 14540 Z= 0.180 Angle : 0.560 5.938 19655 Z= 0.313 Chirality : 0.043 0.158 2230 Planarity : 0.004 0.034 2355 Dihedral : 6.701 57.767 2355 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.33 % Allowed : 6.64 % Favored : 91.03 % 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: 2.29 (0.20), residues: 1660 helix: 2.70 (0.22), residues: 540 sheet: 1.16 (0.24), residues: 435 loop : 0.92 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 349 HIS 0.005 0.001 HIS D 126 PHE 0.018 0.001 PHE E 356 TYR 0.016 0.002 TYR A 340 ARG 0.001 0.000 ARG B 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 10) link_NAG-ASN : angle 1.89541 ( 30) hydrogen bonds : bond 0.08322 ( 695) hydrogen bonds : angle 4.23618 ( 2175) covalent geometry : bond 0.00273 (14530) covalent geometry : angle 0.55560 (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 252 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8737 (mm) cc_final: 0.8195 (tp) REVERT: B 337 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7699 (mtt-85) REVERT: C 281 ILE cc_start: 0.8695 (mm) cc_final: 0.8149 (tp) REVERT: C 304 TRP cc_start: 0.8488 (m100) cc_final: 0.8261 (m-90) REVERT: D 281 ILE cc_start: 0.8710 (mm) cc_final: 0.8463 (mp) REVERT: E 281 ILE cc_start: 0.8714 (mm) cc_final: 0.8176 (tp) outliers start: 35 outliers final: 5 residues processed: 229 average time/residue: 1.4756 time to fit residues: 366.7348 Evaluate side-chains 217 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 212 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain D residue 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: 7.9990 chunk 161 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 199 ASN B 251 GLN B 287 GLN C 199 ASN C 251 GLN D 181 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN E 251 GLN E 287 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.137845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.114487 restraints weight = 11006.279| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 0.85 r_work: 0.3064 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14540 Z= 0.263 Angle : 0.695 5.738 19655 Z= 0.393 Chirality : 0.047 0.208 2230 Planarity : 0.005 0.039 2355 Dihedral : 8.050 59.989 2355 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.59 % Allowed : 6.98 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.83 (0.19), residues: 1660 helix: 2.48 (0.21), residues: 540 sheet: 1.08 (0.25), residues: 370 loop : 0.43 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 349 HIS 0.009 0.002 HIS B 126 PHE 0.022 0.002 PHE D 356 TYR 0.018 0.002 TYR D 340 ARG 0.003 0.000 ARG B 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 10) link_NAG-ASN : angle 1.65130 ( 30) hydrogen bonds : bond 0.10690 ( 695) hydrogen bonds : angle 4.53535 ( 2175) covalent geometry : bond 0.00420 (14530) covalent geometry : angle 0.69225 (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 252 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8868 (mm) cc_final: 0.8369 (tp) REVERT: B 337 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7692 (mtt-85) REVERT: C 281 ILE cc_start: 0.8849 (mm) cc_final: 0.8343 (tp) REVERT: C 304 TRP cc_start: 0.8544 (m100) cc_final: 0.8306 (m-90) REVERT: D 200 MET cc_start: 0.8651 (mtt) cc_final: 0.8401 (mtp) REVERT: D 281 ILE cc_start: 0.8847 (mm) cc_final: 0.8612 (mp) REVERT: E 281 ILE cc_start: 0.8862 (mm) cc_final: 0.8359 (tp) outliers start: 39 outliers final: 14 residues processed: 228 average time/residue: 1.5151 time to fit residues: 374.6954 Evaluate side-chains 224 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 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 122 LEU Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 212 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 145 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN E 199 ASN E 251 GLN E 287 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.138707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.115418 restraints weight = 11159.702| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 0.85 r_work: 0.3077 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 14540 Z= 0.244 Angle : 0.658 5.325 19655 Z= 0.373 Chirality : 0.045 0.168 2230 Planarity : 0.005 0.039 2355 Dihedral : 8.201 59.402 2355 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.79 % Allowed : 7.18 % Favored : 90.03 % 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: 2.49 (0.21), residues: 540 sheet: 1.04 (0.25), residues: 370 loop : 0.38 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 349 HIS 0.008 0.002 HIS D 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 0.00136 ( 10) link_NAG-ASN : angle 1.17028 ( 30) hydrogen bonds : bond 0.10113 ( 695) hydrogen bonds : angle 4.46339 ( 2175) covalent geometry : bond 0.00386 (14530) covalent geometry : angle 0.65713 (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 257 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8865 (mm) cc_final: 0.8363 (tp) REVERT: B 238 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8151 (mptp) REVERT: B 337 ARG cc_start: 0.7893 (mtt180) cc_final: 0.7644 (mtt-85) REVERT: C 281 ILE cc_start: 0.8841 (mm) cc_final: 0.8329 (tp) REVERT: C 304 TRP cc_start: 0.8545 (m100) cc_final: 0.8306 (m-90) REVERT: D 200 MET cc_start: 0.8662 (mtt) cc_final: 0.8402 (mtp) REVERT: D 281 ILE cc_start: 0.8835 (mm) cc_final: 0.8597 (mp) REVERT: E 281 ILE cc_start: 0.8873 (mm) cc_final: 0.8373 (tp) outliers start: 42 outliers final: 19 residues processed: 232 average time/residue: 1.4739 time to fit residues: 370.6100 Evaluate side-chains 233 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 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 158 MET Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 135 optimal weight: 0.0000 chunk 43 optimal weight: 9.9990 chunk 100 optimal weight: 0.0020 chunk 122 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 140 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.145117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.122644 restraints weight = 11465.910| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 0.86 r_work: 0.3177 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 0.019 14540 Z= 0.166 Angle : 0.533 5.157 19655 Z= 0.299 Chirality : 0.042 0.172 2230 Planarity : 0.004 0.035 2355 Dihedral : 7.107 58.085 2355 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.93 % Allowed : 8.64 % Favored : 89.44 % 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: 2.23 (0.20), residues: 1660 helix: 2.76 (0.22), residues: 540 sheet: 1.17 (0.24), residues: 425 loop : 0.76 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 349 HIS 0.005 0.001 HIS D 126 PHE 0.018 0.001 PHE D 356 TYR 0.017 0.002 TYR A 340 ARG 0.002 0.000 ARG C 191 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 10) link_NAG-ASN : angle 0.90463 ( 30) hydrogen bonds : bond 0.07697 ( 695) hydrogen bonds : angle 4.08127 ( 2175) covalent geometry : bond 0.00254 (14530) covalent geometry : angle 0.53247 (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 247 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8789 (mm) cc_final: 0.8291 (tp) REVERT: B 200 MET cc_start: 0.8735 (mtt) cc_final: 0.8445 (mtp) REVERT: B 238 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8068 (mptp) REVERT: B 337 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7616 (mtt-85) REVERT: C 281 ILE cc_start: 0.8761 (mm) cc_final: 0.8260 (tp) REVERT: C 304 TRP cc_start: 0.8532 (m100) cc_final: 0.8294 (m-90) REVERT: D 200 MET cc_start: 0.8628 (mtt) cc_final: 0.8366 (mtp) REVERT: D 281 ILE cc_start: 0.8755 (mm) cc_final: 0.8242 (tp) REVERT: E 281 ILE cc_start: 0.8768 (mm) cc_final: 0.8263 (tp) outliers start: 29 outliers final: 11 residues processed: 231 average time/residue: 1.4007 time to fit residues: 351.4363 Evaluate side-chains 227 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 310 VAL 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: 1.9990 chunk 135 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 7 optimal weight: 0.0570 chunk 131 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 251 GLN C 199 ASN C 251 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN E 181 GLN E 199 ASN E 251 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.144401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.121126 restraints weight = 11416.862| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 0.87 r_work: 0.3159 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1889 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= 0.182 Angle : 0.555 5.156 19655 Z= 0.312 Chirality : 0.043 0.154 2230 Planarity : 0.004 0.035 2355 Dihedral : 7.107 59.144 2355 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.33 % Allowed : 9.10 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.22 (0.20), residues: 1660 helix: 2.75 (0.22), residues: 540 sheet: 1.17 (0.24), residues: 425 loop : 0.75 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 349 HIS 0.005 0.001 HIS E 126 PHE 0.019 0.001 PHE D 356 TYR 0.016 0.002 TYR B 340 ARG 0.001 0.000 ARG B 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 10) link_NAG-ASN : angle 0.82083 ( 30) hydrogen bonds : bond 0.08160 ( 695) hydrogen bonds : angle 4.12250 ( 2175) covalent geometry : bond 0.00278 (14530) covalent geometry : angle 0.55438 (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 252 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8614 (tmt) REVERT: A 281 ILE cc_start: 0.8795 (mm) cc_final: 0.8293 (tp) REVERT: C 281 ILE cc_start: 0.8752 (mm) cc_final: 0.8246 (tp) REVERT: C 304 TRP cc_start: 0.8525 (m100) cc_final: 0.8286 (m-90) REVERT: D 200 MET cc_start: 0.8655 (mtt) cc_final: 0.8392 (mtp) REVERT: D 281 ILE cc_start: 0.8752 (mm) cc_final: 0.8231 (tp) REVERT: E 281 ILE cc_start: 0.8770 (mm) cc_final: 0.8255 (tp) outliers start: 35 outliers final: 16 residues processed: 229 average time/residue: 1.4374 time to fit residues: 357.4615 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 : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 134 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 181 GLN C 199 ASN C 251 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN E 181 GLN E 199 ASN E 251 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.141239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.117723 restraints weight = 11142.921| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 0.86 r_work: 0.3109 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 14540 Z= 0.227 Angle : 0.627 5.410 19655 Z= 0.355 Chirality : 0.045 0.162 2230 Planarity : 0.004 0.037 2355 Dihedral : 7.823 59.073 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 : 2.39 % Allowed : 9.10 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.90 (0.20), residues: 1660 helix: 2.60 (0.21), residues: 540 sheet: 1.10 (0.26), residues: 370 loop : 0.42 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 349 HIS 0.008 0.002 HIS C 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 0.00176 ( 10) link_NAG-ASN : angle 0.79444 ( 30) hydrogen bonds : bond 0.09561 ( 695) hydrogen bonds : angle 4.34770 ( 2175) covalent geometry : bond 0.00355 (14530) covalent geometry : angle 0.62657 (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: 36 poor density : 211 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8845 (mm) cc_final: 0.8344 (tp) REVERT: B 238 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8129 (mptp) REVERT: C 281 ILE cc_start: 0.8821 (mm) cc_final: 0.8304 (tp) REVERT: C 304 TRP cc_start: 0.8548 (m100) cc_final: 0.8310 (m-90) REVERT: D 200 MET cc_start: 0.8679 (mtt) cc_final: 0.8423 (mtp) REVERT: D 281 ILE cc_start: 0.8814 (mm) cc_final: 0.8302 (tp) REVERT: E 281 ILE cc_start: 0.8850 (mm) cc_final: 0.8344 (tp) outliers start: 36 outliers final: 17 residues processed: 227 average time/residue: 1.5021 time to fit residues: 371.0111 Evaluate side-chains 228 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 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 158 MET Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 227 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 105 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN B 199 ASN B 251 GLN C 199 ASN C 251 GLN D 181 GLN D 199 ASN D 287 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 = 0.3518 r_free = 0.3518 target = 0.140702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.117159 restraints weight = 11119.606| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 0.86 r_work: 0.3101 rms_B_bonded: 1.25 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: 0.8578 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 14540 Z= 0.234 Angle : 0.641 5.660 19655 Z= 0.363 Chirality : 0.045 0.164 2230 Planarity : 0.004 0.037 2355 Dihedral : 8.170 58.429 2355 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.99 % Allowed : 9.44 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.83 (0.19), residues: 1660 helix: 2.54 (0.21), residues: 540 sheet: 1.06 (0.26), residues: 370 loop : 0.39 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 349 HIS 0.008 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 0.00176 ( 10) link_NAG-ASN : angle 0.79583 ( 30) hydrogen bonds : bond 0.09820 ( 695) hydrogen bonds : angle 4.38779 ( 2175) covalent geometry : bond 0.00369 (14530) covalent geometry : angle 0.64123 (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 239 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8857 (mm) cc_final: 0.8360 (tp) REVERT: B 238 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8128 (mptp) REVERT: C 281 ILE cc_start: 0.8830 (mm) cc_final: 0.8320 (tp) REVERT: C 304 TRP cc_start: 0.8548 (m100) cc_final: 0.8313 (m-90) REVERT: D 200 MET cc_start: 0.8675 (mtt) cc_final: 0.8410 (mtp) REVERT: D 281 ILE cc_start: 0.8819 (mm) cc_final: 0.8305 (tp) REVERT: E 281 ILE cc_start: 0.8861 (mm) cc_final: 0.8361 (tp) outliers start: 30 outliers final: 17 residues processed: 224 average time/residue: 1.4460 time to fit residues: 351.1132 Evaluate side-chains 228 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 158 MET Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 227 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 5 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.0000 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- 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 287 GLN E 181 GLN E 199 ASN E 251 GLN E 287 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.141639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.118113 restraints weight = 11171.347| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 0.87 r_work: 0.3110 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1851 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= 0.219 Angle : 0.617 5.640 19655 Z= 0.349 Chirality : 0.044 0.159 2230 Planarity : 0.004 0.038 2355 Dihedral : 8.074 58.970 2355 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.73 % Allowed : 9.77 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.56 (0.21), residues: 540 sheet: 1.07 (0.26), residues: 370 loop : 0.41 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 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 0.00205 ( 10) link_NAG-ASN : angle 0.79112 ( 30) hydrogen bonds : bond 0.09421 ( 695) hydrogen bonds : angle 4.33300 ( 2175) covalent geometry : bond 0.00341 (14530) covalent geometry : angle 0.61677 (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 238 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ILE cc_start: 0.8826 (mm) cc_final: 0.8330 (tp) REVERT: B 238 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8108 (mptp) REVERT: C 281 ILE cc_start: 0.8804 (mm) cc_final: 0.8288 (tp) REVERT: C 304 TRP cc_start: 0.8534 (m100) cc_final: 0.8294 (m-90) REVERT: D 200 MET cc_start: 0.8662 (mtt) cc_final: 0.8391 (mtp) REVERT: D 281 ILE cc_start: 0.8802 (mm) cc_final: 0.8286 (tp) REVERT: E 281 ILE cc_start: 0.8839 (mm) cc_final: 0.8344 (tp) outliers start: 26 outliers final: 17 residues processed: 228 average time/residue: 1.5077 time to fit residues: 372.4093 Evaluate side-chains 227 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 1.690 ------------------------------------------------------------------------------- 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 310 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 116 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** D 287 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 = 0.3557 r_free = 0.3557 target = 0.143977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.120674 restraints weight = 11310.762| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 0.87 r_work: 0.3155 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1935 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= 0.189 Angle : 0.570 5.587 19655 Z= 0.320 Chirality : 0.043 0.154 2230 Planarity : 0.004 0.037 2355 Dihedral : 7.623 59.230 2355 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.59 % Allowed : 10.17 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.15 (0.20), residues: 1660 helix: 2.67 (0.22), residues: 540 sheet: 1.36 (0.24), residues: 415 loop : 0.56 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 349 HIS 0.006 0.001 HIS D 126 PHE 0.020 0.002 PHE D 356 TYR 0.016 0.002 TYR A 340 ARG 0.002 0.000 ARG B 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 10) link_NAG-ASN : angle 0.76765 ( 30) hydrogen bonds : bond 0.08436 ( 695) hydrogen bonds : angle 4.18288 ( 2175) covalent geometry : bond 0.00291 (14530) covalent geometry : angle 0.56916 (19625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11911.41 seconds wall clock time: 205 minutes 38.87 seconds (12338.87 seconds total)