Starting phenix.real_space_refine on Wed Feb 4 23:52:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8op9_17045/02_2026/8op9_17045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8op9_17045/02_2026/8op9_17045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8op9_17045/02_2026/8op9_17045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8op9_17045/02_2026/8op9_17045.map" model { file = "/net/cci-nas-00/data/ceres_data/8op9_17045/02_2026/8op9_17045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8op9_17045/02_2026/8op9_17045.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 75 5.16 5 Cl 1 4.86 5 C 9070 2.51 5 N 2195 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13811 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {' CL': 1, 'ABU': 2, 'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Unusual residues: {'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ABU': 2, 'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Unusual residues: {'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {'ABU': 1, 'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.11, per 1000 atoms: 0.23 Number of scatterers: 13811 At special positions: 0 Unit cell: (95.0235, 97.6815, 137.551, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 75 16.00 O 2470 8.00 N 2195 7.00 C 9070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 212 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False 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 501 " - " ASN B 140 " " NAG B 502 " - " ASN B 234 " " NAG C 603 " - " ASN C 140 " " NAG C 604 " - " ASN C 234 " " NAG D 501 " - " ASN D 140 " " NAG D 502 " - " ASN D 234 " " NAG E 602 " - " ASN E 140 " " NAG E 603 " - " ASN E 234 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 495.1 milliseconds 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 41.0% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.601A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 288 through 298 Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.814A pdb=" N SER A 302 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 334 Proline residue: A 315 - end of helix removed outlier: 4.210A pdb=" N SER A 334 " --> pdb=" O GLY A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 380 removed outlier: 3.608A pdb=" N VAL A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 478 removed outlier: 4.072A 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 80 through 84 Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 147 through 153 removed outlier: 3.601A pdb=" N LYS B 151 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 288 through 298 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.814A pdb=" N SER B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 334 Proline residue: B 315 - end of helix removed outlier: 4.210A pdb=" N SER B 334 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 380 removed outlier: 3.609A pdb=" N VAL B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 478 removed outlier: 4.072A 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 80 through 84 Processing helix chain 'C' and resid 131 through 134 Processing helix chain 'C' and resid 147 through 153 removed outlier: 3.600A pdb=" N LYS C 151 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 281 through 288 Processing helix chain 'C' and resid 288 through 298 Processing helix chain 'C' and resid 299 through 304 removed outlier: 3.814A pdb=" N SER C 302 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 334 Proline residue: C 315 - end of helix removed outlier: 4.210A pdb=" N SER C 334 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 380 removed outlier: 3.608A pdb=" N VAL C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 478 removed outlier: 4.072A 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 80 through 84 Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 147 through 153 removed outlier: 3.600A pdb=" N LYS D 151 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 Processing helix chain 'D' and resid 281 through 288 Processing helix chain 'D' and resid 288 through 298 Processing helix chain 'D' and resid 299 through 304 removed outlier: 3.814A pdb=" N SER D 302 " --> pdb=" O SER D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 334 Proline residue: D 315 - end of helix removed outlier: 4.210A pdb=" N SER D 334 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 380 removed outlier: 3.608A pdb=" N VAL D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 478 removed outlier: 4.072A 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 80 through 84 Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 147 through 153 removed outlier: 3.601A pdb=" N LYS E 151 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 281 through 288 Processing helix chain 'E' and resid 288 through 298 Processing helix chain 'E' and resid 299 through 304 removed outlier: 3.814A pdb=" N SER E 302 " --> pdb=" O SER E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 334 Proline residue: E 315 - end of helix removed outlier: 4.210A pdb=" N SER E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 380 removed outlier: 3.609A pdb=" N VAL E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 478 removed outlier: 4.073A 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: 4.460A pdb=" N LEU A 178 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 removed outlier: 7.027A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE A 168 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG A 191 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.002A 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: 4.710A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER A 218 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN A 269 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY A 266 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE A 261 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR A 268 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU A 259 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG A 270 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR A 257 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR A 272 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR A 255 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 274 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.096A 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: 4.460A pdb=" N LEU B 178 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 168 removed outlier: 7.028A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE B 168 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ARG B 191 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.001A 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: 4.709A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER B 218 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN B 269 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY B 266 " --> pdb=" O PHE B 261 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE B 261 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR B 268 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU B 259 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG B 270 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR B 257 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR B 272 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR B 255 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN B 274 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.095A 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: 4.459A pdb=" N LEU C 178 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 163 through 168 removed outlier: 7.028A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE C 168 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG C 191 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.002A 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: 4.710A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER C 218 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN C 269 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY C 266 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE C 261 " --> pdb=" O GLY C 266 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR C 268 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU C 259 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG C 270 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR C 257 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR C 272 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR C 255 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN C 274 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.096A 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: 4.460A pdb=" N LEU D 178 " --> pdb=" O PHE D 145 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 163 through 168 removed outlier: 7.027A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE D 168 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG D 191 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.002A 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: 4.708A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER D 218 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN D 269 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY D 266 " --> pdb=" O PHE D 261 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE D 261 " --> pdb=" O GLY D 266 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR D 268 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU D 259 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG D 270 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR D 257 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR D 272 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR D 255 " --> pdb=" O TYR D 272 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN D 274 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 4.095A 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: 4.460A pdb=" N LEU E 178 " --> pdb=" O PHE E 145 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 163 through 168 removed outlier: 7.028A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE E 168 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG E 191 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.002A 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: 4.709A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER E 218 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN E 269 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY E 266 " --> pdb=" O PHE E 261 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE E 261 " --> pdb=" O GLY E 266 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR E 268 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU E 259 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG E 270 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR E 257 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR E 272 " --> pdb=" O THR E 255 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR E 255 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN E 274 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE E 253 " --> pdb=" O ASN E 274 " (cutoff:3.500A) 785 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4105 1.34 - 1.46: 3298 1.46 - 1.58: 6607 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14150 Sorted by residual: bond pdb=" C2 HEX C 608 " pdb=" C3 HEX C 608 " ideal model delta sigma weight residual 1.524 1.554 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C4 HEX E 607 " pdb=" C5 HEX E 607 " ideal model delta sigma weight residual 1.524 1.554 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C2 HEX E 607 " pdb=" C3 HEX E 607 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C2 HEX D 506 " pdb=" C3 HEX D 506 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C4 HEX C 608 " pdb=" C5 HEX C 608 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.15e+00 ... (remaining 14145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 18138 1.02 - 2.04: 838 2.04 - 3.06: 115 3.06 - 4.08: 72 4.08 - 5.10: 32 Bond angle restraints: 19195 Sorted by residual: angle pdb=" CA TYR E 362 " pdb=" CB TYR E 362 " pdb=" CG TYR E 362 " ideal model delta sigma weight residual 113.90 109.23 4.67 1.80e+00 3.09e-01 6.73e+00 angle pdb=" CA TYR B 362 " pdb=" CB TYR B 362 " pdb=" CG TYR B 362 " ideal model delta sigma weight residual 113.90 109.24 4.66 1.80e+00 3.09e-01 6.69e+00 angle pdb=" CA TYR A 362 " pdb=" CB TYR A 362 " pdb=" CG TYR A 362 " ideal model delta sigma weight residual 113.90 109.25 4.65 1.80e+00 3.09e-01 6.69e+00 angle pdb=" CA TYR C 362 " pdb=" CB TYR C 362 " pdb=" CG TYR C 362 " ideal model delta sigma weight residual 113.90 109.25 4.65 1.80e+00 3.09e-01 6.68e+00 angle pdb=" CA TYR D 362 " pdb=" CB TYR D 362 " pdb=" CG TYR D 362 " ideal model delta sigma weight residual 113.90 109.25 4.65 1.80e+00 3.09e-01 6.66e+00 ... (remaining 19190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 8130 16.19 - 32.38: 215 32.38 - 48.57: 35 48.57 - 64.77: 5 64.77 - 80.96: 10 Dihedral angle restraints: 8395 sinusoidal: 3440 harmonic: 4955 Sorted by residual: dihedral pdb=" CA SER D 107 " pdb=" C SER D 107 " pdb=" N LEU D 108 " pdb=" CA LEU D 108 " ideal model delta harmonic sigma weight residual 180.00 164.27 15.73 0 5.00e+00 4.00e-02 9.90e+00 dihedral pdb=" CA SER A 107 " pdb=" C SER A 107 " pdb=" N LEU A 108 " pdb=" CA LEU A 108 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.85e+00 dihedral pdb=" CA SER B 107 " pdb=" C SER B 107 " pdb=" N LEU B 108 " pdb=" CA LEU B 108 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.85e+00 ... (remaining 8392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1648 0.044 - 0.088: 411 0.088 - 0.132: 136 0.132 - 0.176: 10 0.176 - 0.219: 5 Chirality restraints: 2210 Sorted by residual: chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 140 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 140 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 140 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2207 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.276 2.00e-02 2.50e+03 3.13e-01 1.22e+03 pdb=" CG ASN D 234 " -0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.487 2.00e-02 2.50e+03 pdb=" C1 NAG D 502 " 0.397 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.276 2.00e-02 2.50e+03 3.12e-01 1.22e+03 pdb=" CG ASN A 234 " 0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.486 2.00e-02 2.50e+03 pdb=" C1 NAG A 603 " -0.397 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.276 2.00e-02 2.50e+03 3.12e-01 1.22e+03 pdb=" CG ASN B 234 " -0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.487 2.00e-02 2.50e+03 pdb=" C1 NAG B 502 " 0.397 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 65 2.59 - 3.17: 10774 3.17 - 3.74: 20342 3.74 - 4.32: 29602 4.32 - 4.90: 49441 Nonbonded interactions: 110224 Sorted by model distance: nonbonded pdb=" OD1 ASN C 234 " pdb=" O5 NAG C 604 " model vdw 2.012 3.040 nonbonded pdb=" OD1 ASN D 234 " pdb=" O5 NAG D 502 " model vdw 2.013 3.040 nonbonded pdb=" OD1 ASN A 234 " pdb=" O5 NAG A 603 " model vdw 2.013 3.040 nonbonded pdb=" OD1 ASN B 234 " pdb=" O5 NAG B 502 " model vdw 2.013 3.040 nonbonded pdb=" OD1 ASN E 234 " pdb=" O5 NAG E 603 " model vdw 2.014 3.040 ... (remaining 110219 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 78 through 479 or resid 605 through 606)) selection = (chain 'B' and (resid 78 through 479 or resid 505 through 506)) selection = (chain 'C' and (resid 78 through 479 or resid 605 through 606)) selection = (chain 'D' and (resid 78 through 479 or resid 505 through 506)) selection = (chain 'E' and (resid 78 through 479 or resid 605 through 606)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.390 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.910 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 : 0.003 0.102 14165 Z= 0.173 Angle : 0.786 20.481 19235 Z= 0.342 Chirality : 0.043 0.219 2210 Planarity : 0.004 0.029 2330 Dihedral : 8.964 80.958 5160 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.21), residues: 1640 helix: 1.73 (0.21), residues: 600 sheet: 1.63 (0.24), residues: 395 loop : 0.94 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 374 TYR 0.019 0.001 TYR D 362 PHE 0.010 0.001 PHE D 253 TRP 0.006 0.001 TRP A 475 HIS 0.002 0.000 HIS E 84 Details of bonding type rmsd covalent geometry : bond 0.00266 (14150) covalent geometry : angle 0.54633 (19195) SS BOND : bond 0.00031 ( 5) SS BOND : angle 0.66968 ( 10) hydrogen bonds : bond 0.17589 ( 690) hydrogen bonds : angle 5.71757 ( 2205) link_NAG-ASN : bond 0.07173 ( 10) link_NAG-ASN : angle 14.29987 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 331 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.8107 (m) cc_final: 0.7868 (p) REVERT: C 143 MET cc_start: 0.7993 (mmm) cc_final: 0.7779 (mmt) REVERT: D 326 THR cc_start: 0.7879 (m) cc_final: 0.7652 (p) REVERT: D 349 TRP cc_start: 0.6951 (m100) cc_final: 0.6481 (m100) REVERT: E 335 MET cc_start: 0.4174 (mmm) cc_final: 0.3965 (mpp) outliers start: 5 outliers final: 0 residues processed: 336 average time/residue: 0.1105 time to fit residues: 53.2330 Evaluate side-chains 215 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN C 247 GLN C 287 GLN D 247 GLN D 287 GLN E 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.154016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131591 restraints weight = 15383.276| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.01 r_work: 0.3298 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14165 Z= 0.157 Angle : 0.612 6.547 19235 Z= 0.321 Chirality : 0.047 0.311 2210 Planarity : 0.004 0.056 2330 Dihedral : 7.272 85.919 2115 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.23 % Allowed : 6.40 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1640 helix: 1.82 (0.21), residues: 600 sheet: 1.17 (0.25), residues: 400 loop : 0.31 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 313 TYR 0.020 0.002 TYR E 127 PHE 0.016 0.002 PHE D 159 TRP 0.015 0.002 TRP D 230 HIS 0.004 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00335 (14150) covalent geometry : angle 0.60130 (19195) SS BOND : bond 0.00377 ( 5) SS BOND : angle 0.73105 ( 10) hydrogen bonds : bond 0.05715 ( 690) hydrogen bonds : angle 3.82500 ( 2205) link_NAG-ASN : bond 0.00655 ( 10) link_NAG-ASN : angle 2.87854 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7918 (ptp90) cc_final: 0.7711 (ptp90) REVERT: A 158 MET cc_start: 0.8062 (mmm) cc_final: 0.7791 (mmm) REVERT: B 158 MET cc_start: 0.8058 (mmm) cc_final: 0.7842 (mmm) REVERT: B 278 ARG cc_start: 0.8258 (mtp180) cc_final: 0.8030 (mtp-110) REVERT: C 158 MET cc_start: 0.7877 (mmm) cc_final: 0.7623 (mmm) REVERT: D 155 VAL cc_start: 0.8521 (t) cc_final: 0.8299 (m) REVERT: D 185 LYS cc_start: 0.8437 (mttp) cc_final: 0.8207 (mmmm) REVERT: D 200 MET cc_start: 0.8289 (mtp) cc_final: 0.8063 (mtm) REVERT: D 203 SER cc_start: 0.8516 (t) cc_final: 0.7522 (p) REVERT: E 85 ASP cc_start: 0.7430 (p0) cc_final: 0.7157 (p0) REVERT: E 115 ASP cc_start: 0.7533 (m-30) cc_final: 0.6909 (m-30) REVERT: E 148 ARG cc_start: 0.7604 (ptt-90) cc_final: 0.7363 (ptt-90) REVERT: E 322 LEU cc_start: 0.7384 (tt) cc_final: 0.6965 (mt) REVERT: E 324 MET cc_start: 0.7427 (tpp) cc_final: 0.7124 (tpt) REVERT: E 335 MET cc_start: 0.4628 (mmm) cc_final: 0.4134 (mmt) outliers start: 48 outliers final: 29 residues processed: 239 average time/residue: 0.1157 time to fit residues: 39.0006 Evaluate side-chains 214 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 92 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.141934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.119350 restraints weight = 15372.669| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.98 r_work: 0.3148 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14165 Z= 0.199 Angle : 0.616 9.712 19235 Z= 0.328 Chirality : 0.049 0.400 2210 Planarity : 0.005 0.046 2330 Dihedral : 6.850 87.971 2115 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.50 % Allowed : 7.47 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1640 helix: 1.64 (0.21), residues: 600 sheet: 1.04 (0.25), residues: 395 loop : -0.03 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 313 TYR 0.023 0.002 TYR E 362 PHE 0.016 0.002 PHE D 284 TRP 0.009 0.001 TRP E 230 HIS 0.006 0.002 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00475 (14150) covalent geometry : angle 0.60919 (19195) SS BOND : bond 0.00757 ( 5) SS BOND : angle 1.94682 ( 10) hydrogen bonds : bond 0.06817 ( 690) hydrogen bonds : angle 3.99101 ( 2205) link_NAG-ASN : bond 0.00451 ( 10) link_NAG-ASN : angle 2.17062 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7952 (ptp90) cc_final: 0.7532 (ptp90) REVERT: B 116 MET cc_start: 0.7935 (mtm) cc_final: 0.7733 (mtp) REVERT: B 278 ARG cc_start: 0.8280 (mtp180) cc_final: 0.8036 (mtp-110) REVERT: B 308 ARG cc_start: 0.7452 (mtm-85) cc_final: 0.7175 (mtp180) REVERT: B 337 ARG cc_start: 0.7408 (mtm180) cc_final: 0.7185 (mtt90) REVERT: C 113 GLU cc_start: 0.8079 (mp0) cc_final: 0.7731 (mp0) REVERT: C 115 ASP cc_start: 0.7838 (m-30) cc_final: 0.7472 (m-30) REVERT: C 148 ARG cc_start: 0.7948 (ptt-90) cc_final: 0.7720 (ptt-90) REVERT: D 158 MET cc_start: 0.8105 (mmm) cc_final: 0.7888 (mmm) REVERT: D 203 SER cc_start: 0.8587 (t) cc_final: 0.7762 (p) REVERT: E 85 ASP cc_start: 0.7654 (p0) cc_final: 0.7448 (p0) REVERT: E 115 ASP cc_start: 0.8010 (m-30) cc_final: 0.7538 (m-30) REVERT: E 265 THR cc_start: 0.7444 (p) cc_final: 0.7144 (p) REVERT: E 298 LEU cc_start: 0.8151 (mt) cc_final: 0.7921 (tt) REVERT: E 335 MET cc_start: 0.5225 (mmm) cc_final: 0.4535 (mmt) outliers start: 52 outliers final: 36 residues processed: 253 average time/residue: 0.1220 time to fit residues: 43.2312 Evaluate side-chains 228 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 340 TYR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 340 TYR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 0.0270 chunk 87 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 152 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.146748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.124555 restraints weight = 15325.201| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.95 r_work: 0.3216 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14165 Z= 0.108 Angle : 0.488 7.865 19235 Z= 0.260 Chirality : 0.043 0.253 2210 Planarity : 0.004 0.041 2330 Dihedral : 6.522 87.432 2115 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.29 % Allowed : 10.37 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.20), residues: 1640 helix: 1.98 (0.21), residues: 600 sheet: 1.07 (0.25), residues: 390 loop : 0.01 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 313 TYR 0.019 0.001 TYR E 362 PHE 0.012 0.001 PHE B 282 TRP 0.008 0.001 TRP B 230 HIS 0.002 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00222 (14150) covalent geometry : angle 0.48269 (19195) SS BOND : bond 0.00358 ( 5) SS BOND : angle 1.30120 ( 10) hydrogen bonds : bond 0.04744 ( 690) hydrogen bonds : angle 3.60146 ( 2205) link_NAG-ASN : bond 0.00528 ( 10) link_NAG-ASN : angle 1.82113 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7879 (ptp90) cc_final: 0.7516 (ptp90) REVERT: A 375 LYS cc_start: 0.7216 (mtpt) cc_final: 0.6982 (ttpt) REVERT: B 200 MET cc_start: 0.8291 (mtm) cc_final: 0.8019 (mtm) REVERT: B 265 THR cc_start: 0.7531 (p) cc_final: 0.7253 (p) REVERT: B 308 ARG cc_start: 0.7471 (mtm-85) cc_final: 0.7189 (mtp180) REVERT: B 337 ARG cc_start: 0.7456 (mtm180) cc_final: 0.7232 (mtt90) REVERT: C 113 GLU cc_start: 0.8036 (mp0) cc_final: 0.7660 (mp0) REVERT: C 185 LYS cc_start: 0.8419 (mttp) cc_final: 0.8137 (mmmm) REVERT: C 457 LYS cc_start: 0.7867 (tttt) cc_final: 0.7616 (tptt) REVERT: D 185 LYS cc_start: 0.8521 (mttp) cc_final: 0.8126 (mtpp) REVERT: D 203 SER cc_start: 0.8569 (t) cc_final: 0.7824 (p) REVERT: D 457 LYS cc_start: 0.7771 (tttt) cc_final: 0.7528 (tptt) REVERT: E 85 ASP cc_start: 0.7662 (p0) cc_final: 0.7411 (p0) REVERT: E 115 ASP cc_start: 0.7895 (m-30) cc_final: 0.7450 (m-30) REVERT: E 170 ASP cc_start: 0.7980 (t0) cc_final: 0.7358 (p0) REVERT: E 308 ARG cc_start: 0.6720 (mtm180) cc_final: 0.6476 (mtt-85) outliers start: 34 outliers final: 24 residues processed: 217 average time/residue: 0.1404 time to fit residues: 41.5692 Evaluate side-chains 215 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 11 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.144632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.122228 restraints weight = 15378.042| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.00 r_work: 0.3188 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14165 Z= 0.133 Angle : 0.515 6.826 19235 Z= 0.273 Chirality : 0.044 0.264 2210 Planarity : 0.004 0.042 2330 Dihedral : 6.242 83.631 2115 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.10 % Allowed : 9.63 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.20), residues: 1640 helix: 1.99 (0.21), residues: 600 sheet: 0.90 (0.25), residues: 410 loop : -0.04 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 148 TYR 0.020 0.002 TYR E 362 PHE 0.012 0.001 PHE E 205 TRP 0.009 0.001 TRP B 128 HIS 0.004 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00303 (14150) covalent geometry : angle 0.50908 (19195) SS BOND : bond 0.00451 ( 5) SS BOND : angle 1.47995 ( 10) hydrogen bonds : bond 0.05188 ( 690) hydrogen bonds : angle 3.58393 ( 2205) link_NAG-ASN : bond 0.00491 ( 10) link_NAG-ASN : angle 1.86412 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7901 (ptp90) cc_final: 0.7515 (ptp90) REVERT: A 375 LYS cc_start: 0.7183 (mtpt) cc_final: 0.6978 (ttpt) REVERT: B 113 GLU cc_start: 0.8181 (mp0) cc_final: 0.7930 (mp0) REVERT: B 265 THR cc_start: 0.7621 (p) cc_final: 0.7359 (p) REVERT: B 308 ARG cc_start: 0.7457 (mtm-85) cc_final: 0.7170 (mtp180) REVERT: B 335 MET cc_start: 0.6149 (tpt) cc_final: 0.5364 (tmm) REVERT: B 337 ARG cc_start: 0.7469 (mtm180) cc_final: 0.7206 (mtt90) REVERT: C 113 GLU cc_start: 0.8053 (mp0) cc_final: 0.7629 (mp0) REVERT: D 148 ARG cc_start: 0.7971 (ptt-90) cc_final: 0.7752 (ptt-90) REVERT: D 185 LYS cc_start: 0.8535 (mttp) cc_final: 0.8134 (mtpp) REVERT: D 203 SER cc_start: 0.8748 (t) cc_final: 0.7940 (p) REVERT: D 457 LYS cc_start: 0.7958 (tttt) cc_final: 0.7660 (tptt) REVERT: E 85 ASP cc_start: 0.7728 (p0) cc_final: 0.7474 (p0) REVERT: E 115 ASP cc_start: 0.7893 (m-30) cc_final: 0.7446 (m-30) REVERT: E 170 ASP cc_start: 0.7918 (t0) cc_final: 0.7501 (p0) REVERT: E 235 ASP cc_start: 0.7499 (m-30) cc_final: 0.6837 (t0) REVERT: E 298 LEU cc_start: 0.8034 (mt) cc_final: 0.7673 (tt) REVERT: E 308 ARG cc_start: 0.6858 (mtm180) cc_final: 0.6636 (mtt-85) outliers start: 46 outliers final: 39 residues processed: 230 average time/residue: 0.1362 time to fit residues: 42.7660 Evaluate side-chains 233 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.138831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116494 restraints weight = 15442.284| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.00 r_work: 0.3113 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14165 Z= 0.233 Angle : 0.619 5.915 19235 Z= 0.330 Chirality : 0.047 0.245 2210 Planarity : 0.005 0.044 2330 Dihedral : 6.257 70.880 2115 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.64 % Allowed : 10.10 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1640 helix: 1.54 (0.21), residues: 600 sheet: 0.62 (0.25), residues: 390 loop : -0.45 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 148 TYR 0.023 0.002 TYR E 362 PHE 0.017 0.002 PHE C 159 TRP 0.012 0.002 TRP E 230 HIS 0.006 0.002 HIS E 280 Details of bonding type rmsd covalent geometry : bond 0.00570 (14150) covalent geometry : angle 0.61411 (19195) SS BOND : bond 0.00691 ( 5) SS BOND : angle 2.07925 ( 10) hydrogen bonds : bond 0.06640 ( 690) hydrogen bonds : angle 3.94593 ( 2205) link_NAG-ASN : bond 0.00436 ( 10) link_NAG-ASN : angle 1.67253 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.6969 (t0) cc_final: 0.6636 (t0) REVERT: A 148 ARG cc_start: 0.8027 (ptp90) cc_final: 0.7617 (ptp90) REVERT: A 278 ARG cc_start: 0.8260 (mtp180) cc_final: 0.8017 (mtp-110) REVERT: A 375 LYS cc_start: 0.7274 (mtpt) cc_final: 0.7072 (ttpt) REVERT: B 308 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.7184 (mtp180) REVERT: C 113 GLU cc_start: 0.8192 (mp0) cc_final: 0.7986 (mp0) REVERT: C 115 ASP cc_start: 0.7864 (m-30) cc_final: 0.7519 (m-30) REVERT: C 298 LEU cc_start: 0.8296 (tp) cc_final: 0.7979 (tt) REVERT: D 203 SER cc_start: 0.8740 (t) cc_final: 0.7987 (p) REVERT: D 284 PHE cc_start: 0.7685 (m-80) cc_final: 0.7416 (m-80) REVERT: E 115 ASP cc_start: 0.7889 (m-30) cc_final: 0.7485 (m-30) REVERT: E 235 ASP cc_start: 0.7793 (m-30) cc_final: 0.7110 (t0) REVERT: E 298 LEU cc_start: 0.8057 (mt) cc_final: 0.7707 (tt) REVERT: E 308 ARG cc_start: 0.6914 (mtm180) cc_final: 0.6695 (mtt-85) REVERT: E 324 MET cc_start: 0.7682 (tpp) cc_final: 0.7410 (tpp) outliers start: 54 outliers final: 44 residues processed: 244 average time/residue: 0.1228 time to fit residues: 41.8220 Evaluate side-chains 248 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.139466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.117532 restraints weight = 15745.804| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.98 r_work: 0.3124 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14165 Z= 0.173 Angle : 0.556 6.567 19235 Z= 0.295 Chirality : 0.045 0.234 2210 Planarity : 0.004 0.045 2330 Dihedral : 5.721 58.606 2115 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.23 % Allowed : 10.98 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1640 helix: 1.62 (0.21), residues: 600 sheet: 0.60 (0.26), residues: 390 loop : -0.44 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 148 TYR 0.019 0.002 TYR E 362 PHE 0.013 0.001 PHE E 205 TRP 0.011 0.001 TRP E 230 HIS 0.005 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00416 (14150) covalent geometry : angle 0.55034 (19195) SS BOND : bond 0.00616 ( 5) SS BOND : angle 1.75616 ( 10) hydrogen bonds : bond 0.05877 ( 690) hydrogen bonds : angle 3.81054 ( 2205) link_NAG-ASN : bond 0.00457 ( 10) link_NAG-ASN : angle 1.92967 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.6965 (t0) cc_final: 0.6638 (t0) REVERT: A 148 ARG cc_start: 0.7842 (ptp90) cc_final: 0.7442 (ptp90) REVERT: A 278 ARG cc_start: 0.8049 (mtp180) cc_final: 0.7805 (mtp-110) REVERT: B 265 THR cc_start: 0.7511 (p) cc_final: 0.7230 (p) REVERT: B 308 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.7125 (mtp180) REVERT: C 112 SER cc_start: 0.7868 (t) cc_final: 0.7141 (t) REVERT: C 113 GLU cc_start: 0.8001 (mp0) cc_final: 0.7749 (mp0) REVERT: C 115 ASP cc_start: 0.7371 (m-30) cc_final: 0.6864 (m-30) REVERT: C 164 LYS cc_start: 0.8833 (mtpp) cc_final: 0.8531 (mtpp) REVERT: D 148 ARG cc_start: 0.7889 (ptt-90) cc_final: 0.7583 (ptt-90) REVERT: D 203 SER cc_start: 0.8570 (t) cc_final: 0.7745 (p) REVERT: E 115 ASP cc_start: 0.7545 (m-30) cc_final: 0.7101 (m-30) REVERT: E 148 ARG cc_start: 0.7711 (ptt-90) cc_final: 0.7426 (ptt-90) REVERT: E 235 ASP cc_start: 0.7634 (m-30) cc_final: 0.6868 (t0) REVERT: E 298 LEU cc_start: 0.7656 (mt) cc_final: 0.7340 (tt) REVERT: E 308 ARG cc_start: 0.6870 (mtm180) cc_final: 0.6230 (mtm-85) REVERT: E 324 MET cc_start: 0.7418 (tpp) cc_final: 0.7166 (tpp) outliers start: 48 outliers final: 41 residues processed: 228 average time/residue: 0.1164 time to fit residues: 36.8770 Evaluate side-chains 238 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 129 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.142086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.119644 restraints weight = 15621.412| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.04 r_work: 0.3149 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14165 Z= 0.125 Angle : 0.508 5.771 19235 Z= 0.268 Chirality : 0.043 0.221 2210 Planarity : 0.004 0.046 2330 Dihedral : 5.241 48.680 2115 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.90 % Allowed : 11.25 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1640 helix: 1.85 (0.21), residues: 600 sheet: 0.67 (0.26), residues: 390 loop : -0.31 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 313 TYR 0.017 0.001 TYR E 362 PHE 0.012 0.001 PHE B 282 TRP 0.009 0.001 TRP C 128 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00284 (14150) covalent geometry : angle 0.50326 (19195) SS BOND : bond 0.00476 ( 5) SS BOND : angle 1.41288 ( 10) hydrogen bonds : bond 0.05084 ( 690) hydrogen bonds : angle 3.64033 ( 2205) link_NAG-ASN : bond 0.00455 ( 10) link_NAG-ASN : angle 1.62456 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.6954 (t0) cc_final: 0.6643 (t0) REVERT: A 148 ARG cc_start: 0.7753 (ptp90) cc_final: 0.7361 (ptp90) REVERT: B 148 ARG cc_start: 0.7582 (ptt180) cc_final: 0.7308 (ptt90) REVERT: B 265 THR cc_start: 0.7394 (p) cc_final: 0.7108 (p) REVERT: B 308 ARG cc_start: 0.7389 (mtm-85) cc_final: 0.7117 (mtp180) REVERT: C 112 SER cc_start: 0.7851 (t) cc_final: 0.7166 (t) REVERT: C 113 GLU cc_start: 0.7938 (mp0) cc_final: 0.7683 (mp0) REVERT: C 115 ASP cc_start: 0.7259 (m-30) cc_final: 0.6825 (m-30) REVERT: C 164 LYS cc_start: 0.8821 (mtpp) cc_final: 0.8533 (mtpp) REVERT: C 185 LYS cc_start: 0.8274 (mttp) cc_final: 0.7821 (mtmt) REVERT: C 457 LYS cc_start: 0.7889 (tttt) cc_final: 0.7186 (ttpp) REVERT: D 148 ARG cc_start: 0.7799 (ptt-90) cc_final: 0.7473 (ptt-90) REVERT: D 185 LYS cc_start: 0.8283 (mttp) cc_final: 0.7816 (mtpp) REVERT: D 203 SER cc_start: 0.8574 (t) cc_final: 0.7727 (p) REVERT: D 457 LYS cc_start: 0.7763 (tttt) cc_final: 0.7150 (ttpp) REVERT: E 148 ARG cc_start: 0.7710 (ptt-90) cc_final: 0.7406 (ptt-90) REVERT: E 235 ASP cc_start: 0.7684 (m-30) cc_final: 0.6835 (t0) REVERT: E 298 LEU cc_start: 0.7564 (mt) cc_final: 0.7284 (tt) REVERT: E 308 ARG cc_start: 0.6856 (mtm180) cc_final: 0.6572 (mtt-85) outliers start: 43 outliers final: 42 residues processed: 236 average time/residue: 0.1292 time to fit residues: 41.6493 Evaluate side-chains 244 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.144370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.121374 restraints weight = 15451.074| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.08 r_work: 0.3173 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14165 Z= 0.117 Angle : 0.502 7.581 19235 Z= 0.264 Chirality : 0.043 0.211 2210 Planarity : 0.004 0.045 2330 Dihedral : 5.079 42.562 2115 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.76 % Allowed : 11.85 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1640 helix: 1.98 (0.21), residues: 600 sheet: 0.57 (0.25), residues: 410 loop : -0.29 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 148 TYR 0.017 0.001 TYR E 362 PHE 0.012 0.001 PHE B 282 TRP 0.010 0.001 TRP C 128 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00263 (14150) covalent geometry : angle 0.49487 (19195) SS BOND : bond 0.00455 ( 5) SS BOND : angle 1.34302 ( 10) hydrogen bonds : bond 0.04769 ( 690) hydrogen bonds : angle 3.52992 ( 2205) link_NAG-ASN : bond 0.00494 ( 10) link_NAG-ASN : angle 2.13060 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.6888 (t0) cc_final: 0.6643 (t0) REVERT: A 148 ARG cc_start: 0.7875 (ptp90) cc_final: 0.7517 (ptp90) REVERT: B 148 ARG cc_start: 0.7668 (ptt180) cc_final: 0.7231 (ptt90) REVERT: B 265 THR cc_start: 0.7549 (p) cc_final: 0.7279 (p) REVERT: B 308 ARG cc_start: 0.7408 (mtm-85) cc_final: 0.7127 (mtp180) REVERT: C 112 SER cc_start: 0.8265 (t) cc_final: 0.7553 (t) REVERT: C 113 GLU cc_start: 0.8048 (mp0) cc_final: 0.7580 (mp0) REVERT: C 115 ASP cc_start: 0.7513 (m-30) cc_final: 0.7167 (m-30) REVERT: C 148 ARG cc_start: 0.7971 (ptt-90) cc_final: 0.7741 (ptt-90) REVERT: C 164 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8695 (mtpp) REVERT: C 185 LYS cc_start: 0.8515 (mttp) cc_final: 0.8161 (mtmt) REVERT: C 457 LYS cc_start: 0.8014 (tttt) cc_final: 0.7312 (ttpp) REVERT: D 148 ARG cc_start: 0.7963 (ptt-90) cc_final: 0.7640 (ptt-90) REVERT: D 185 LYS cc_start: 0.8555 (mttp) cc_final: 0.8139 (mtpp) REVERT: D 203 SER cc_start: 0.8726 (t) cc_final: 0.7932 (p) REVERT: D 337 ARG cc_start: 0.7219 (mtm180) cc_final: 0.6531 (mpt-90) REVERT: D 457 LYS cc_start: 0.8003 (tttt) cc_final: 0.7420 (ttpp) REVERT: E 148 ARG cc_start: 0.7828 (ptt-90) cc_final: 0.7532 (ptt-90) REVERT: E 235 ASP cc_start: 0.7798 (m-30) cc_final: 0.7001 (t0) REVERT: E 298 LEU cc_start: 0.7903 (mt) cc_final: 0.7667 (tt) REVERT: E 308 ARG cc_start: 0.6914 (mtm180) cc_final: 0.6653 (mtt-85) REVERT: E 375 LYS cc_start: 0.7077 (mtpt) cc_final: 0.6790 (ttpt) outliers start: 41 outliers final: 39 residues processed: 235 average time/residue: 0.1246 time to fit residues: 40.2723 Evaluate side-chains 240 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 50 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 0.0570 chunk 111 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.144988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.122113 restraints weight = 15397.339| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.07 r_work: 0.3180 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14165 Z= 0.117 Angle : 0.497 6.129 19235 Z= 0.262 Chirality : 0.042 0.199 2210 Planarity : 0.004 0.043 2330 Dihedral : 4.843 39.661 2115 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.83 % Allowed : 12.19 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.21), residues: 1640 helix: 2.07 (0.21), residues: 600 sheet: 0.59 (0.25), residues: 410 loop : -0.25 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 148 TYR 0.017 0.001 TYR E 362 PHE 0.012 0.001 PHE B 282 TRP 0.011 0.001 TRP C 128 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00264 (14150) covalent geometry : angle 0.49169 (19195) SS BOND : bond 0.00455 ( 5) SS BOND : angle 1.31237 ( 10) hydrogen bonds : bond 0.04651 ( 690) hydrogen bonds : angle 3.49582 ( 2205) link_NAG-ASN : bond 0.00406 ( 10) link_NAG-ASN : angle 1.68049 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.6868 (t0) cc_final: 0.6635 (t0) REVERT: A 148 ARG cc_start: 0.7876 (ptp90) cc_final: 0.7526 (ptp90) REVERT: A 335 MET cc_start: 0.5749 (tpp) cc_final: 0.5083 (tmm) REVERT: B 148 ARG cc_start: 0.7662 (ptt180) cc_final: 0.7369 (ptt90) REVERT: B 265 THR cc_start: 0.7548 (p) cc_final: 0.7274 (p) REVERT: B 308 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.6955 (mtp85) REVERT: C 112 SER cc_start: 0.8259 (t) cc_final: 0.7584 (t) REVERT: C 113 GLU cc_start: 0.8072 (mp0) cc_final: 0.7593 (mp0) REVERT: C 115 ASP cc_start: 0.7579 (m-30) cc_final: 0.7204 (m-30) REVERT: C 148 ARG cc_start: 0.7872 (ptt-90) cc_final: 0.7584 (ptt-90) REVERT: C 337 ARG cc_start: 0.7417 (mtm180) cc_final: 0.7083 (mtt180) REVERT: D 148 ARG cc_start: 0.7946 (ptt-90) cc_final: 0.7612 (ptt-90) REVERT: D 185 LYS cc_start: 0.8555 (mttp) cc_final: 0.8125 (mtpp) REVERT: D 203 SER cc_start: 0.8718 (t) cc_final: 0.7947 (p) REVERT: D 337 ARG cc_start: 0.7262 (mtm180) cc_final: 0.6997 (mtt180) REVERT: D 457 LYS cc_start: 0.7978 (tttt) cc_final: 0.7394 (ttpp) REVERT: E 148 ARG cc_start: 0.7824 (ptt-90) cc_final: 0.7525 (ptt-90) REVERT: E 235 ASP cc_start: 0.7803 (m-30) cc_final: 0.7038 (t0) REVERT: E 308 ARG cc_start: 0.6905 (mtm180) cc_final: 0.6625 (mtp180) REVERT: E 375 LYS cc_start: 0.7060 (mtpt) cc_final: 0.6780 (ttpt) outliers start: 42 outliers final: 40 residues processed: 226 average time/residue: 0.1249 time to fit residues: 39.1197 Evaluate side-chains 234 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 159 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.144175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.121314 restraints weight = 15382.574| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.06 r_work: 0.3171 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14165 Z= 0.127 Angle : 0.511 8.947 19235 Z= 0.268 Chirality : 0.043 0.195 2210 Planarity : 0.004 0.042 2330 Dihedral : 4.843 40.865 2115 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.03 % Allowed : 12.12 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.20), residues: 1640 helix: 2.04 (0.21), residues: 600 sheet: 0.68 (0.26), residues: 390 loop : -0.34 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 148 TYR 0.018 0.001 TYR E 362 PHE 0.012 0.001 PHE E 205 TRP 0.010 0.001 TRP C 128 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00292 (14150) covalent geometry : angle 0.50746 (19195) SS BOND : bond 0.00480 ( 5) SS BOND : angle 1.39960 ( 10) hydrogen bonds : bond 0.04839 ( 690) hydrogen bonds : angle 3.52169 ( 2205) link_NAG-ASN : bond 0.00388 ( 10) link_NAG-ASN : angle 1.43570 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2850.17 seconds wall clock time: 49 minutes 34.94 seconds (2974.94 seconds total)