Starting phenix.real_space_refine on Sat Oct 11 10:45:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8op9_17045/10_2025/8op9_17045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8op9_17045/10_2025/8op9_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 { model { file = "/net/cci-nas-00/data/ceres_data/8op9_17045/10_2025/8op9_17045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8op9_17045/10_2025/8op9_17045.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8op9_17045/10_2025/8op9_17045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8op9_17045/10_2025/8op9_17045.map" } 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-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13811 Number of models: 1 Model: "" Number of chains: 12 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: "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: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} 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} Restraints were copied for chains: E, C, D Time building chain proxies: 3.70, per 1000 atoms: 0.27 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 E 198 " - pdb=" SG CYS E 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 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 538.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.54 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: 3.06 Time building geometry restraints manager: 1.32 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: 7.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.270 Find NCS groups from input model: 0.460 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:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.950 ------------------------------------------------------------------------------- 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 aren 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 : 0.573 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: 0.1379 time to fit residues: 65.6638 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 : 0.462 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131640 restraints weight = 15383.276| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.99 r_work: 0.3303 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 aren 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 : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7919 (ptp90) cc_final: 0.7714 (ptp90) REVERT: A 158 MET cc_start: 0.8062 (mmm) cc_final: 0.7794 (mmm) REVERT: B 158 MET cc_start: 0.8056 (mmm) cc_final: 0.7842 (mmm) REVERT: B 278 ARG cc_start: 0.8254 (mtp180) cc_final: 0.8029 (mtp-110) REVERT: C 158 MET cc_start: 0.7877 (mmm) cc_final: 0.7625 (mmm) REVERT: D 155 VAL cc_start: 0.8527 (t) cc_final: 0.8304 (m) REVERT: D 185 LYS cc_start: 0.8442 (mttp) cc_final: 0.8213 (mmmm) REVERT: D 200 MET cc_start: 0.8291 (mtp) cc_final: 0.8068 (mtm) REVERT: D 203 SER cc_start: 0.8518 (t) cc_final: 0.7526 (p) REVERT: E 85 ASP cc_start: 0.7432 (p0) cc_final: 0.7158 (p0) REVERT: E 115 ASP cc_start: 0.7538 (m-30) cc_final: 0.6914 (m-30) REVERT: E 148 ARG cc_start: 0.7608 (ptt-90) cc_final: 0.7369 (ptt-90) REVERT: E 322 LEU cc_start: 0.7393 (tt) cc_final: 0.6975 (mt) REVERT: E 324 MET cc_start: 0.7432 (tpp) cc_final: 0.7129 (tpt) REVERT: E 335 MET cc_start: 0.4625 (mmm) cc_final: 0.4133 (mmt) outliers start: 48 outliers final: 29 residues processed: 239 average time/residue: 0.1309 time to fit residues: 44.2291 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 : 0.551 ------------------------------------------------------------------------------- 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: 0.0050 chunk 37 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.3800 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.142220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.119535 restraints weight = 15355.421| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.98 r_work: 0.3152 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14165 Z= 0.190 Angle : 0.606 10.240 19235 Z= 0.322 Chirality : 0.048 0.381 2210 Planarity : 0.005 0.041 2330 Dihedral : 6.826 87.714 2115 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.50 % Allowed : 7.54 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.20), residues: 1640 helix: 1.70 (0.21), residues: 600 sheet: 1.07 (0.25), residues: 395 loop : -0.03 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 148 TYR 0.024 0.002 TYR E 362 PHE 0.016 0.002 PHE C 159 TRP 0.009 0.001 TRP E 128 HIS 0.006 0.002 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00445 (14150) covalent geometry : angle 0.60058 (19195) SS BOND : bond 0.00406 ( 5) SS BOND : angle 1.25612 ( 10) hydrogen bonds : bond 0.06678 ( 690) hydrogen bonds : angle 3.97359 ( 2205) link_NAG-ASN : bond 0.00902 ( 10) link_NAG-ASN : angle 1.98873 ( 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 270 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7939 (ptp90) cc_final: 0.7499 (ptp90) REVERT: A 375 LYS cc_start: 0.7383 (mtpt) cc_final: 0.7139 (ttpt) REVERT: B 278 ARG cc_start: 0.8277 (mtp180) cc_final: 0.8074 (mtp-110) REVERT: B 308 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7144 (mtp180) REVERT: B 337 ARG cc_start: 0.7397 (mtm180) cc_final: 0.7179 (mtt90) REVERT: C 113 GLU cc_start: 0.8053 (mp0) cc_final: 0.7698 (mp0) REVERT: C 115 ASP cc_start: 0.7800 (m-30) cc_final: 0.7413 (m-30) REVERT: D 148 ARG cc_start: 0.8168 (ptt-90) cc_final: 0.7879 (ptt-90) REVERT: D 158 MET cc_start: 0.8096 (mmm) cc_final: 0.7887 (mmm) REVERT: D 203 SER cc_start: 0.8576 (t) cc_final: 0.7761 (p) REVERT: E 115 ASP cc_start: 0.8003 (m-30) cc_final: 0.7548 (m-30) REVERT: E 265 THR cc_start: 0.7435 (p) cc_final: 0.7138 (p) REVERT: E 298 LEU cc_start: 0.8134 (mt) cc_final: 0.7915 (tt) REVERT: E 335 MET cc_start: 0.5199 (mmm) cc_final: 0.4518 (mmt) outliers start: 52 outliers final: 34 residues processed: 249 average time/residue: 0.1435 time to fit residues: 49.8598 Evaluate side-chains 224 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 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 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 293 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 D residue 371 VAL Chi-restraints excluded: chain E residue 189 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: 0.0000 chunk 87 optimal weight: 0.0050 chunk 12 optimal weight: 2.9990 chunk 152 optimal weight: 0.0020 chunk 40 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.3206 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.147766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.125446 restraints weight = 15315.110| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.95 r_work: 0.3228 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14165 Z= 0.103 Angle : 0.490 10.777 19235 Z= 0.259 Chirality : 0.043 0.251 2210 Planarity : 0.004 0.041 2330 Dihedral : 6.506 87.497 2115 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.82 % Allowed : 10.91 % 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 aren not related in a simple way. whole: 1.49 (0.20), residues: 1640 helix: 2.02 (0.21), residues: 600 sheet: 1.01 (0.25), residues: 395 loop : 0.06 (0.23), residues: 645 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 0.011 0.001 PHE B 282 TRP 0.008 0.001 TRP E 128 HIS 0.002 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00203 (14150) covalent geometry : angle 0.48307 (19195) SS BOND : bond 0.00298 ( 5) SS BOND : angle 1.12640 ( 10) hydrogen bonds : bond 0.04592 ( 690) hydrogen bonds : angle 3.56116 ( 2205) link_NAG-ASN : bond 0.00535 ( 10) link_NAG-ASN : angle 2.06989 ( 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 225 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7861 (ptp90) cc_final: 0.7482 (ptp90) REVERT: A 375 LYS cc_start: 0.7093 (mtpt) cc_final: 0.6870 (ttpt) REVERT: B 265 THR cc_start: 0.7434 (p) cc_final: 0.7160 (p) REVERT: B 278 ARG cc_start: 0.8180 (mtp180) cc_final: 0.7971 (mtp-110) REVERT: B 308 ARG cc_start: 0.7474 (mtm-85) cc_final: 0.7194 (mtp180) REVERT: B 335 MET cc_start: 0.6162 (tpt) cc_final: 0.5377 (tmm) REVERT: B 337 ARG cc_start: 0.7407 (mtm180) cc_final: 0.7188 (mtt90) REVERT: C 113 GLU cc_start: 0.7979 (mp0) cc_final: 0.7600 (mp0) REVERT: C 185 LYS cc_start: 0.8355 (mttp) cc_final: 0.8064 (mmmm) REVERT: C 457 LYS cc_start: 0.7790 (tttt) cc_final: 0.7513 (tptt) REVERT: D 148 ARG cc_start: 0.7907 (ptt-90) cc_final: 0.7632 (ptt-90) REVERT: D 185 LYS cc_start: 0.8451 (mttp) cc_final: 0.8041 (mtpp) REVERT: D 203 SER cc_start: 0.8529 (t) cc_final: 0.7754 (p) REVERT: D 457 LYS cc_start: 0.7691 (tttt) cc_final: 0.7443 (tptt) REVERT: E 85 ASP cc_start: 0.7674 (p0) cc_final: 0.7447 (p0) REVERT: E 115 ASP cc_start: 0.7833 (m-30) cc_final: 0.7365 (m-30) REVERT: E 170 ASP cc_start: 0.7778 (t0) cc_final: 0.7071 (p0) REVERT: E 308 ARG cc_start: 0.6715 (mtm180) cc_final: 0.6474 (mtt-85) REVERT: E 335 MET cc_start: 0.5165 (mmm) cc_final: 0.4534 (mmt) outliers start: 27 outliers final: 21 residues processed: 215 average time/residue: 0.1565 time to fit residues: 45.6020 Evaluate side-chains 214 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 365 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 177 MET 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 E residue 114 VAL 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: 0.5980 chunk 9 optimal weight: 0.0970 chunk 102 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.144992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.122546 restraints weight = 15376.272| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.01 r_work: 0.3196 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4474 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= 0.132 Angle : 0.514 9.008 19235 Z= 0.271 Chirality : 0.043 0.259 2210 Planarity : 0.004 0.045 2330 Dihedral : 6.249 83.803 2115 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.23 % Allowed : 10.03 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.20), residues: 1640 helix: 2.00 (0.21), residues: 600 sheet: 0.89 (0.25), residues: 395 loop : -0.06 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 148 TYR 0.020 0.001 TYR E 362 PHE 0.011 0.001 PHE B 159 TRP 0.010 0.001 TRP B 128 HIS 0.004 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00302 (14150) covalent geometry : angle 0.50681 (19195) SS BOND : bond 0.00577 ( 5) SS BOND : angle 1.65820 ( 10) hydrogen bonds : bond 0.05092 ( 690) hydrogen bonds : angle 3.55582 ( 2205) link_NAG-ASN : bond 0.00475 ( 10) link_NAG-ASN : angle 2.03416 ( 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 243 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7912 (ptp90) cc_final: 0.7518 (ptp90) REVERT: A 375 LYS cc_start: 0.7175 (mtpt) cc_final: 0.6971 (ttpt) REVERT: B 113 GLU cc_start: 0.8111 (mp0) cc_final: 0.7895 (mp0) REVERT: B 265 THR cc_start: 0.7615 (p) cc_final: 0.7346 (p) REVERT: B 308 ARG cc_start: 0.7456 (mtm-85) cc_final: 0.7171 (mtp180) REVERT: B 337 ARG cc_start: 0.7440 (mtm180) cc_final: 0.7190 (mtt90) REVERT: C 113 GLU cc_start: 0.8029 (mp0) cc_final: 0.7612 (mp0) REVERT: D 185 LYS cc_start: 0.8519 (mttp) cc_final: 0.8111 (mtpp) REVERT: D 203 SER cc_start: 0.8737 (t) cc_final: 0.7911 (p) REVERT: D 457 LYS cc_start: 0.7933 (tttt) cc_final: 0.7638 (tptt) REVERT: E 85 ASP cc_start: 0.7834 (p0) cc_final: 0.7544 (p0) REVERT: E 115 ASP cc_start: 0.7886 (m-30) cc_final: 0.7439 (m-30) REVERT: E 148 ARG cc_start: 0.7699 (ptt-90) cc_final: 0.7474 (ptt-90) REVERT: E 170 ASP cc_start: 0.7780 (t0) cc_final: 0.7186 (p0) REVERT: E 235 ASP cc_start: 0.7471 (m-30) cc_final: 0.6831 (t0) REVERT: E 298 LEU cc_start: 0.8031 (mt) cc_final: 0.7678 (tt) REVERT: E 308 ARG cc_start: 0.6870 (mtm180) cc_final: 0.6642 (mtt-85) outliers start: 48 outliers final: 39 residues processed: 225 average time/residue: 0.1513 time to fit residues: 46.8746 Evaluate side-chains 228 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 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 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 D residue 371 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 174 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.138327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.116135 restraints weight = 15445.030| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.99 r_work: 0.3106 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14165 Z= 0.259 Angle : 0.636 7.824 19235 Z= 0.339 Chirality : 0.048 0.250 2210 Planarity : 0.005 0.049 2330 Dihedral : 6.354 69.753 2115 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.50 % Allowed : 10.57 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.20), residues: 1640 helix: 1.50 (0.21), residues: 600 sheet: 0.63 (0.26), residues: 375 loop : -0.48 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 148 TYR 0.025 0.002 TYR E 362 PHE 0.017 0.002 PHE C 159 TRP 0.012 0.002 TRP E 230 HIS 0.007 0.002 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00638 (14150) covalent geometry : angle 0.63109 (19195) SS BOND : bond 0.00764 ( 5) SS BOND : angle 2.14247 ( 10) hydrogen bonds : bond 0.06871 ( 690) hydrogen bonds : angle 4.01588 ( 2205) link_NAG-ASN : bond 0.00413 ( 10) link_NAG-ASN : angle 1.83744 ( 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 261 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.6985 (t0) cc_final: 0.6660 (t0) REVERT: A 148 ARG cc_start: 0.8040 (ptp90) cc_final: 0.7616 (ptp90) REVERT: A 278 ARG cc_start: 0.8266 (mtp180) cc_final: 0.8014 (mtp-110) REVERT: A 375 LYS cc_start: 0.7282 (mtpt) cc_final: 0.7077 (ttpt) REVERT: B 308 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.7166 (mtp180) REVERT: C 115 ASP cc_start: 0.7894 (m-30) cc_final: 0.7551 (m-30) REVERT: C 298 LEU cc_start: 0.8302 (tp) cc_final: 0.7981 (tt) REVERT: D 203 SER cc_start: 0.8718 (t) cc_final: 0.7970 (p) REVERT: D 284 PHE cc_start: 0.7689 (m-80) cc_final: 0.7419 (m-80) REVERT: E 115 ASP cc_start: 0.7871 (m-30) cc_final: 0.7444 (m-30) REVERT: E 235 ASP cc_start: 0.7791 (m-30) cc_final: 0.7111 (t0) REVERT: E 298 LEU cc_start: 0.8031 (mt) cc_final: 0.7688 (tt) REVERT: E 308 ARG cc_start: 0.6943 (mtm180) cc_final: 0.6714 (mtt-85) REVERT: E 324 MET cc_start: 0.7671 (tpp) cc_final: 0.7401 (tpp) outliers start: 52 outliers final: 44 residues processed: 242 average time/residue: 0.1515 time to fit residues: 50.6497 Evaluate side-chains 247 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 203 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 176 VAL 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 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: 0.8980 chunk 82 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.141439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.119678 restraints weight = 15720.923| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.96 r_work: 0.3153 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14165 Z= 0.131 Angle : 0.521 8.666 19235 Z= 0.275 Chirality : 0.043 0.229 2210 Planarity : 0.004 0.047 2330 Dihedral : 5.612 58.434 2115 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.69 % Allowed : 11.85 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.20), residues: 1640 helix: 1.79 (0.21), residues: 600 sheet: 0.49 (0.25), residues: 415 loop : -0.25 (0.23), residues: 625 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 0.009 0.001 TRP E 230 HIS 0.004 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00296 (14150) covalent geometry : angle 0.51440 (19195) SS BOND : bond 0.00525 ( 5) SS BOND : angle 1.57943 ( 10) hydrogen bonds : bond 0.05318 ( 690) hydrogen bonds : angle 3.70825 ( 2205) link_NAG-ASN : bond 0.00466 ( 10) link_NAG-ASN : angle 1.96206 ( 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 250 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.6900 (t0) cc_final: 0.6602 (t0) REVERT: A 148 ARG cc_start: 0.7820 (ptp90) cc_final: 0.7427 (ptp90) REVERT: B 200 MET cc_start: 0.8338 (mtm) cc_final: 0.8057 (mtm) REVERT: B 265 THR cc_start: 0.7437 (p) cc_final: 0.7156 (p) REVERT: B 308 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.7109 (mtp180) REVERT: B 335 MET cc_start: 0.6363 (tpt) cc_final: 0.5537 (tmm) REVERT: C 112 SER cc_start: 0.7941 (t) cc_final: 0.7220 (t) REVERT: C 115 ASP cc_start: 0.7321 (m-30) cc_final: 0.6895 (m-30) REVERT: C 148 ARG cc_start: 0.7857 (ptt-90) cc_final: 0.7564 (ptt-90) REVERT: C 164 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8535 (mtpp) REVERT: C 185 LYS cc_start: 0.8306 (mttp) cc_final: 0.8047 (mmmm) REVERT: C 457 LYS cc_start: 0.7904 (tttt) cc_final: 0.7203 (ttpp) REVERT: D 185 LYS cc_start: 0.8298 (mttp) cc_final: 0.7830 (mtpp) REVERT: D 203 SER cc_start: 0.8581 (t) cc_final: 0.7736 (p) REVERT: D 457 LYS cc_start: 0.7828 (tttt) cc_final: 0.7222 (ttpp) REVERT: E 170 ASP cc_start: 0.7446 (t0) cc_final: 0.6846 (p0) REVERT: E 235 ASP cc_start: 0.7632 (m-30) cc_final: 0.6857 (t0) REVERT: E 298 LEU cc_start: 0.7660 (mt) cc_final: 0.7377 (tt) REVERT: E 308 ARG cc_start: 0.6846 (mtm180) cc_final: 0.6230 (mtm-85) REVERT: E 335 MET cc_start: 0.5649 (tpt) cc_final: 0.5029 (tmm) outliers start: 40 outliers final: 37 residues processed: 238 average time/residue: 0.1541 time to fit residues: 50.6084 Evaluate side-chains 239 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 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 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: 0.0870 chunk 145 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.141880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.119468 restraints weight = 15586.147| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.04 r_work: 0.3146 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14165 Z= 0.132 Angle : 0.520 8.698 19235 Z= 0.273 Chirality : 0.043 0.221 2210 Planarity : 0.004 0.047 2330 Dihedral : 5.250 49.159 2115 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.56 % Allowed : 11.78 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.20), residues: 1640 helix: 1.88 (0.21), residues: 600 sheet: 0.61 (0.26), residues: 395 loop : -0.28 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 148 TYR 0.019 0.001 TYR E 362 PHE 0.012 0.001 PHE E 205 TRP 0.010 0.001 TRP C 128 HIS 0.004 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00303 (14150) covalent geometry : angle 0.51581 (19195) SS BOND : bond 0.00480 ( 5) SS BOND : angle 1.46894 ( 10) hydrogen bonds : bond 0.05144 ( 690) hydrogen bonds : angle 3.61776 ( 2205) link_NAG-ASN : bond 0.00468 ( 10) link_NAG-ASN : angle 1.59224 ( 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 235 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.6884 (t0) cc_final: 0.6629 (t0) REVERT: A 88 MET cc_start: 0.8721 (mtt) cc_final: 0.8446 (mpp) REVERT: A 148 ARG cc_start: 0.7792 (ptp90) cc_final: 0.7401 (ptp90) REVERT: B 148 ARG cc_start: 0.7684 (ptt-90) cc_final: 0.7286 (ptt90) REVERT: B 200 MET cc_start: 0.8397 (mtm) cc_final: 0.8148 (mtm) REVERT: B 265 THR cc_start: 0.7487 (p) cc_final: 0.7199 (p) REVERT: B 308 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.7096 (mtp180) REVERT: B 335 MET cc_start: 0.6304 (tpt) cc_final: 0.5591 (tmm) REVERT: C 115 ASP cc_start: 0.7448 (m-30) cc_final: 0.7134 (m-30) REVERT: C 164 LYS cc_start: 0.8852 (mtpp) cc_final: 0.8574 (mtpp) REVERT: D 148 ARG cc_start: 0.7914 (ptt-90) cc_final: 0.7704 (ptt-90) REVERT: D 185 LYS cc_start: 0.8354 (mttp) cc_final: 0.7902 (mtpp) REVERT: D 203 SER cc_start: 0.8610 (t) cc_final: 0.7778 (p) REVERT: D 457 LYS cc_start: 0.7863 (tttt) cc_final: 0.7254 (ttpp) REVERT: E 143 MET cc_start: 0.7651 (mmt) cc_final: 0.7247 (mmt) REVERT: E 148 ARG cc_start: 0.7675 (ptt-90) cc_final: 0.7409 (ptt-90) REVERT: E 235 ASP cc_start: 0.7726 (m-30) cc_final: 0.6900 (t0) REVERT: E 298 LEU cc_start: 0.7690 (mt) cc_final: 0.7429 (tt) REVERT: E 308 ARG cc_start: 0.6890 (mtm180) cc_final: 0.6591 (mtt-85) REVERT: E 335 MET cc_start: 0.5744 (tpt) cc_final: 0.5208 (tmm) outliers start: 38 outliers final: 38 residues processed: 224 average time/residue: 0.1544 time to fit residues: 47.6032 Evaluate side-chains 234 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 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 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: 0.9990 chunk 49 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.143480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.120648 restraints weight = 15425.674| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.06 r_work: 0.3162 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14165 Z= 0.128 Angle : 0.518 10.125 19235 Z= 0.271 Chirality : 0.043 0.212 2210 Planarity : 0.004 0.046 2330 Dihedral : 5.136 43.480 2115 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.90 % Allowed : 11.72 % 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 aren not related in a simple way. whole: 1.12 (0.20), residues: 1640 helix: 1.95 (0.21), residues: 600 sheet: 0.56 (0.25), residues: 410 loop : -0.25 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 148 TYR 0.018 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 0.00293 (14150) covalent geometry : angle 0.50965 (19195) SS BOND : bond 0.00485 ( 5) SS BOND : angle 1.43413 ( 10) hydrogen bonds : bond 0.04956 ( 690) hydrogen bonds : angle 3.57191 ( 2205) link_NAG-ASN : bond 0.00427 ( 10) link_NAG-ASN : angle 2.22065 ( 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 237 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.6855 (t0) cc_final: 0.6624 (t0) REVERT: A 148 ARG cc_start: 0.7885 (ptp90) cc_final: 0.7526 (ptp90) REVERT: B 148 ARG cc_start: 0.7752 (ptt-90) cc_final: 0.7329 (ptt90) REVERT: B 265 THR cc_start: 0.7649 (p) cc_final: 0.7376 (p) REVERT: B 308 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7126 (mtp180) REVERT: C 115 ASP cc_start: 0.7524 (m-30) cc_final: 0.7254 (m-30) REVERT: C 148 ARG cc_start: 0.7941 (ptt-90) cc_final: 0.7723 (ptt-90) REVERT: C 164 LYS cc_start: 0.8937 (mtpp) cc_final: 0.8703 (mtpp) REVERT: D 158 MET cc_start: 0.8142 (mmm) cc_final: 0.7930 (mmm) REVERT: D 185 LYS cc_start: 0.8559 (mttp) cc_final: 0.8134 (mtpp) REVERT: D 203 SER cc_start: 0.8719 (t) cc_final: 0.7933 (p) REVERT: D 457 LYS cc_start: 0.8034 (tttt) cc_final: 0.7445 (ttpp) REVERT: E 148 ARG cc_start: 0.7749 (ptt-90) cc_final: 0.7316 (ptt90) REVERT: E 235 ASP cc_start: 0.7794 (m-30) cc_final: 0.7019 (t0) REVERT: E 298 LEU cc_start: 0.7936 (mt) cc_final: 0.7689 (tt) REVERT: E 308 ARG cc_start: 0.6987 (mtm180) cc_final: 0.6711 (mtt-85) REVERT: E 335 MET cc_start: 0.5845 (tpt) cc_final: 0.5353 (tmm) outliers start: 43 outliers final: 40 residues processed: 224 average time/residue: 0.1526 time to fit residues: 47.4187 Evaluate side-chains 231 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 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 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 246 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 50 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.144280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.121486 restraints weight = 15354.991| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.04 r_work: 0.3174 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14165 Z= 0.121 Angle : 0.502 6.613 19235 Z= 0.265 Chirality : 0.043 0.202 2210 Planarity : 0.004 0.045 2330 Dihedral : 4.947 43.494 2115 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.69 % Allowed : 12.39 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.20), residues: 1640 helix: 2.02 (0.21), residues: 600 sheet: 0.52 (0.25), residues: 415 loop : -0.22 (0.24), residues: 625 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 0.010 0.001 TRP C 128 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00277 (14150) covalent geometry : angle 0.49670 (19195) SS BOND : bond 0.00468 ( 5) SS BOND : angle 1.39432 ( 10) hydrogen bonds : bond 0.04784 ( 690) hydrogen bonds : angle 3.52544 ( 2205) link_NAG-ASN : bond 0.00406 ( 10) link_NAG-ASN : angle 1.76856 ( 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 234 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.6836 (t0) cc_final: 0.6388 (t0) REVERT: A 148 ARG cc_start: 0.7894 (ptp90) cc_final: 0.7539 (ptp90) REVERT: A 335 MET cc_start: 0.6002 (tpp) cc_final: 0.5680 (tpp) REVERT: B 148 ARG cc_start: 0.7768 (ptt-90) cc_final: 0.7368 (ptt90) REVERT: B 265 THR cc_start: 0.7615 (p) cc_final: 0.7339 (p) REVERT: B 308 ARG cc_start: 0.7399 (mtm-85) cc_final: 0.7122 (mtp180) REVERT: C 115 ASP cc_start: 0.7574 (m-30) cc_final: 0.7318 (m-30) REVERT: C 164 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8695 (mtpp) REVERT: C 337 ARG cc_start: 0.7419 (mtm180) cc_final: 0.7090 (mtt180) REVERT: D 158 MET cc_start: 0.8177 (mmm) cc_final: 0.7974 (mmm) REVERT: D 185 LYS cc_start: 0.8552 (mttp) cc_final: 0.8130 (mtpp) REVERT: D 203 SER cc_start: 0.8713 (t) cc_final: 0.7929 (p) REVERT: D 337 ARG cc_start: 0.7234 (mtm180) cc_final: 0.6539 (mpt-90) REVERT: D 457 LYS cc_start: 0.7996 (tttt) cc_final: 0.7411 (ttpp) REVERT: E 148 ARG cc_start: 0.7713 (ptt-90) cc_final: 0.7405 (ptt90) REVERT: E 235 ASP cc_start: 0.7776 (m-30) cc_final: 0.6994 (t0) REVERT: E 298 LEU cc_start: 0.7939 (mt) cc_final: 0.7706 (tt) REVERT: E 308 ARG cc_start: 0.6967 (mtm180) cc_final: 0.6660 (mtp180) REVERT: E 335 MET cc_start: 0.5740 (tpt) cc_final: 0.5315 (tmm) REVERT: E 375 LYS cc_start: 0.7116 (mtpt) cc_final: 0.6898 (ttpt) outliers start: 40 outliers final: 39 residues processed: 223 average time/residue: 0.1618 time to fit residues: 49.2098 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 : 0.532 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 123 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.144698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.121889 restraints weight = 15379.745| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.05 r_work: 0.3178 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14165 Z= 0.117 Angle : 0.498 6.627 19235 Z= 0.262 Chirality : 0.042 0.194 2210 Planarity : 0.004 0.043 2330 Dihedral : 4.836 40.816 2115 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.96 % Allowed : 12.26 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.21), residues: 1640 helix: 2.01 (0.21), residues: 605 sheet: 0.53 (0.25), residues: 415 loop : -0.17 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 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 0.00266 (14150) covalent geometry : angle 0.49420 (19195) SS BOND : bond 0.00453 ( 5) SS BOND : angle 1.34992 ( 10) hydrogen bonds : bond 0.04678 ( 690) hydrogen bonds : angle 3.49885 ( 2205) link_NAG-ASN : bond 0.00388 ( 10) link_NAG-ASN : angle 1.43370 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3393.55 seconds wall clock time: 59 minutes 1.79 seconds (3541.79 seconds total)