Starting phenix.real_space_refine on Fri May 16 04:00:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8op9_17045/05_2025/8op9_17045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8op9_17045/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8op9_17045/05_2025/8op9_17045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8op9_17045/05_2025/8op9_17045.map" model { file = "/net/cci-nas-00/data/ceres_data/8op9_17045/05_2025/8op9_17045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8op9_17045/05_2025/8op9_17045.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} 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: 11.06, per 1000 atoms: 0.80 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: 3.80 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.89 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: 4.50 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4105 1.34 - 1.46: 3298 1.46 - 1.58: 6607 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14150 Sorted by residual: bond pdb=" C2 HEX C 608 " pdb=" C3 HEX C 608 " ideal model delta sigma weight residual 1.524 1.554 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C4 HEX E 607 " pdb=" C5 HEX E 607 " ideal model delta sigma weight residual 1.524 1.554 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C2 HEX E 607 " pdb=" C3 HEX E 607 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C2 HEX D 506 " pdb=" C3 HEX D 506 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C4 HEX C 608 " pdb=" C5 HEX C 608 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.15e+00 ... (remaining 14145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 18138 1.02 - 2.04: 838 2.04 - 3.06: 115 3.06 - 4.08: 72 4.08 - 5.10: 32 Bond angle restraints: 19195 Sorted by residual: angle pdb=" CA TYR E 362 " pdb=" CB TYR E 362 " pdb=" CG TYR E 362 " ideal model delta sigma weight residual 113.90 109.23 4.67 1.80e+00 3.09e-01 6.73e+00 angle pdb=" CA TYR B 362 " pdb=" CB TYR B 362 " pdb=" CG TYR B 362 " ideal model delta sigma weight residual 113.90 109.24 4.66 1.80e+00 3.09e-01 6.69e+00 angle pdb=" CA TYR A 362 " pdb=" CB TYR A 362 " pdb=" CG TYR A 362 " ideal model delta sigma weight residual 113.90 109.25 4.65 1.80e+00 3.09e-01 6.69e+00 angle pdb=" CA TYR C 362 " pdb=" CB TYR C 362 " pdb=" CG TYR C 362 " ideal model delta sigma weight residual 113.90 109.25 4.65 1.80e+00 3.09e-01 6.68e+00 angle pdb=" CA TYR D 362 " pdb=" CB TYR D 362 " pdb=" CG TYR D 362 " ideal model delta sigma weight residual 113.90 109.25 4.65 1.80e+00 3.09e-01 6.66e+00 ... (remaining 19190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 8130 16.19 - 32.38: 215 32.38 - 48.57: 35 48.57 - 64.77: 5 64.77 - 80.96: 10 Dihedral angle restraints: 8395 sinusoidal: 3440 harmonic: 4955 Sorted by residual: dihedral pdb=" CA SER D 107 " pdb=" C SER D 107 " pdb=" N LEU D 108 " pdb=" CA LEU D 108 " ideal model delta harmonic sigma weight residual 180.00 164.27 15.73 0 5.00e+00 4.00e-02 9.90e+00 dihedral pdb=" CA SER A 107 " pdb=" C SER A 107 " pdb=" N LEU A 108 " pdb=" CA LEU A 108 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.85e+00 dihedral pdb=" CA SER B 107 " pdb=" C SER B 107 " pdb=" N LEU B 108 " pdb=" CA LEU B 108 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.85e+00 ... (remaining 8392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1648 0.044 - 0.088: 411 0.088 - 0.132: 136 0.132 - 0.176: 10 0.176 - 0.219: 5 Chirality restraints: 2210 Sorted by residual: chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 140 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 140 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 140 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2207 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.276 2.00e-02 2.50e+03 3.13e-01 1.22e+03 pdb=" CG ASN D 234 " -0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.487 2.00e-02 2.50e+03 pdb=" C1 NAG D 502 " 0.397 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.276 2.00e-02 2.50e+03 3.12e-01 1.22e+03 pdb=" CG ASN A 234 " 0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.486 2.00e-02 2.50e+03 pdb=" C1 NAG A 603 " -0.397 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.276 2.00e-02 2.50e+03 3.12e-01 1.22e+03 pdb=" CG ASN B 234 " -0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.487 2.00e-02 2.50e+03 pdb=" C1 NAG B 502 " 0.397 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 65 2.59 - 3.17: 10774 3.17 - 3.74: 20342 3.74 - 4.32: 29602 4.32 - 4.90: 49441 Nonbonded interactions: 110224 Sorted by model distance: nonbonded pdb=" OD1 ASN C 234 " pdb=" O5 NAG C 604 " model vdw 2.012 3.040 nonbonded pdb=" OD1 ASN D 234 " pdb=" O5 NAG D 502 " model vdw 2.013 3.040 nonbonded pdb=" OD1 ASN A 234 " pdb=" O5 NAG A 603 " model vdw 2.013 3.040 nonbonded pdb=" OD1 ASN B 234 " pdb=" O5 NAG B 502 " model vdw 2.013 3.040 nonbonded pdb=" OD1 ASN E 234 " pdb=" O5 NAG E 603 " model vdw 2.014 3.040 ... (remaining 110219 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 78 through 479 or resid 605 through 606)) selection = (chain 'B' and (resid 78 through 479 or resid 505 through 506)) selection = (chain 'C' and (resid 78 through 479 or resid 605 through 606)) selection = (chain 'D' and (resid 78 through 479 or resid 505 through 506)) selection = (chain 'E' and (resid 78 through 479 or resid 605 through 606)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 37.230 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (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 TRP 0.006 0.001 TRP A 475 HIS 0.002 0.000 HIS E 84 PHE 0.010 0.001 PHE D 253 TYR 0.019 0.001 TYR D 362 ARG 0.003 0.001 ARG D 374 Details of bonding type rmsd link_NAG-ASN : bond 0.07173 ( 10) link_NAG-ASN : angle 14.29987 ( 30) hydrogen bonds : bond 0.17589 ( 690) hydrogen bonds : angle 5.71757 ( 2205) SS BOND : bond 0.00031 ( 5) SS BOND : angle 0.66968 ( 10) covalent geometry : bond 0.00266 (14150) covalent geometry : angle 0.54633 (19195) *********************** 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 : 1.492 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: 0.7869 (p) REVERT: C 143 MET cc_start: 0.7993 (mmm) cc_final: 0.7782 (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: 0.2837 time to fit residues: 134.7331 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 : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.7980 chunk 125 optimal weight: 0.1980 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 GLN C 287 GLN D 247 GLN D 287 GLN E 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.144711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.122617 restraints weight = 15537.338| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.95 r_work: 0.3198 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14165 Z= 0.218 Angle : 0.686 7.777 19235 Z= 0.361 Chirality : 0.051 0.340 2210 Planarity : 0.005 0.053 2330 Dihedral : 7.609 88.262 2115 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 3.64 % Allowed : 5.93 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1640 helix: 1.39 (0.20), residues: 600 sheet: 1.02 (0.25), residues: 400 loop : 0.15 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 230 HIS 0.008 0.002 HIS C 280 PHE 0.022 0.002 PHE D 159 TYR 0.024 0.002 TYR E 188 ARG 0.011 0.001 ARG E 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 10) link_NAG-ASN : angle 2.73502 ( 30) hydrogen bonds : bond 0.06940 ( 690) hydrogen bonds : angle 4.04177 ( 2205) SS BOND : bond 0.00400 ( 5) SS BOND : angle 1.39565 ( 10) covalent geometry : bond 0.00508 (14150) covalent geometry : angle 0.67727 (19195) *********************** 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 291 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7928 (ptp90) cc_final: 0.7663 (ptp90) REVERT: A 158 MET cc_start: 0.8077 (mmm) cc_final: 0.7763 (mmm) REVERT: A 278 ARG cc_start: 0.8007 (mtp180) cc_final: 0.7727 (mtp-110) REVERT: B 151 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7750 (mmtm) REVERT: B 158 MET cc_start: 0.8063 (mmm) cc_final: 0.7785 (mmm) REVERT: B 200 MET cc_start: 0.8003 (mtm) cc_final: 0.7773 (mtm) REVERT: B 278 ARG cc_start: 0.8104 (mtp180) cc_final: 0.7867 (mtp-110) REVERT: C 115 ASP cc_start: 0.7624 (m-30) cc_final: 0.7310 (m-30) REVERT: C 158 MET cc_start: 0.7854 (mmm) cc_final: 0.7554 (mmm) REVERT: D 115 ASP cc_start: 0.7613 (m-30) cc_final: 0.7297 (m-30) REVERT: D 185 LYS cc_start: 0.8282 (mttp) cc_final: 0.7861 (mtpp) REVERT: D 203 SER cc_start: 0.8351 (t) cc_final: 0.7401 (p) REVERT: E 115 ASP cc_start: 0.7605 (m-30) cc_final: 0.6949 (m-30) REVERT: E 235 ASP cc_start: 0.6912 (m-30) cc_final: 0.6448 (t0) REVERT: E 322 LEU cc_start: 0.7191 (tt) cc_final: 0.6878 (mp) REVERT: E 335 MET cc_start: 0.4906 (mmm) cc_final: 0.4243 (mmt) outliers start: 54 outliers final: 31 residues processed: 269 average time/residue: 0.3070 time to fit residues: 113.9502 Evaluate side-chains 242 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 87 SER 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 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 151 LYS 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 236 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 338 VAL 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 236 SER Chi-restraints excluded: chain D residue 302 SER 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 319 THR Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 100 optimal weight: 0.0270 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 82 optimal weight: 0.0060 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.148280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.126141 restraints weight = 15327.186| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.96 r_work: 0.3238 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14165 Z= 0.115 Angle : 0.501 10.222 19235 Z= 0.267 Chirality : 0.045 0.346 2210 Planarity : 0.004 0.045 2330 Dihedral : 6.612 89.529 2115 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.63 % Allowed : 9.16 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.20), residues: 1640 helix: 2.02 (0.21), residues: 600 sheet: 1.10 (0.25), residues: 415 loop : 0.22 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 230 HIS 0.002 0.001 HIS A 254 PHE 0.013 0.001 PHE A 282 TYR 0.018 0.001 TYR E 362 ARG 0.004 0.000 ARG E 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 10) link_NAG-ASN : angle 1.85494 ( 30) hydrogen bonds : bond 0.05190 ( 690) hydrogen bonds : angle 3.71516 ( 2205) SS BOND : bond 0.00166 ( 5) SS BOND : angle 0.87679 ( 10) covalent geometry : bond 0.00243 (14150) covalent geometry : angle 0.49589 (19195) *********************** 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 248 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7856 (ptp90) cc_final: 0.7467 (ptp90) REVERT: A 375 LYS cc_start: 0.7395 (mtpt) cc_final: 0.7118 (ttpt) REVERT: B 88 MET cc_start: 0.8911 (mtm) cc_final: 0.8710 (mpp) REVERT: B 148 ARG cc_start: 0.7765 (ptp90) cc_final: 0.7287 (ptp90) REVERT: B 200 MET cc_start: 0.8372 (mtm) cc_final: 0.8154 (mtm) REVERT: B 265 THR cc_start: 0.7585 (p) cc_final: 0.7284 (p) REVERT: B 308 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.7152 (mtp180) REVERT: B 337 ARG cc_start: 0.7404 (mtm180) cc_final: 0.7148 (mtt90) REVERT: C 148 ARG cc_start: 0.7779 (ptt-90) cc_final: 0.7558 (ptt-90) REVERT: C 158 MET cc_start: 0.7955 (mmm) cc_final: 0.7696 (mmm) REVERT: C 185 LYS cc_start: 0.8396 (mttp) cc_final: 0.8160 (mmmm) REVERT: C 457 LYS cc_start: 0.7738 (tttt) cc_final: 0.7493 (tptt) REVERT: D 185 LYS cc_start: 0.8457 (mttp) cc_final: 0.8216 (mmmm) REVERT: D 197 MET cc_start: 0.7319 (mtm) cc_final: 0.7098 (mtt) REVERT: D 203 SER cc_start: 0.8552 (t) cc_final: 0.7636 (p) REVERT: D 457 LYS cc_start: 0.7750 (tttp) cc_final: 0.7504 (tptt) REVERT: E 85 ASP cc_start: 0.7647 (p0) cc_final: 0.7428 (p0) REVERT: E 115 ASP cc_start: 0.7935 (m-30) cc_final: 0.7566 (m-30) REVERT: E 148 ARG cc_start: 0.7596 (ptt-90) cc_final: 0.7353 (ptt-90) REVERT: E 308 ARG cc_start: 0.6634 (mtm180) cc_final: 0.6388 (mtt-85) REVERT: E 335 MET cc_start: 0.5182 (mmm) cc_final: 0.4562 (mmt) outliers start: 39 outliers final: 24 residues processed: 234 average time/residue: 0.3168 time to fit residues: 101.6741 Evaluate side-chains 220 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 236 SER 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 236 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 265 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 96 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.146140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.123903 restraints weight = 15337.467| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.95 r_work: 0.3208 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4064 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 : 0.497 6.214 19235 Z= 0.265 Chirality : 0.044 0.268 2210 Planarity : 0.004 0.038 2330 Dihedral : 6.489 89.862 2115 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.16 % Allowed : 8.69 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.20), residues: 1640 helix: 2.05 (0.21), residues: 600 sheet: 0.99 (0.25), residues: 415 loop : 0.07 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.003 0.001 HIS C 280 PHE 0.011 0.001 PHE A 282 TYR 0.018 0.001 TYR A 362 ARG 0.004 0.000 ARG E 179 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 10) link_NAG-ASN : angle 1.65493 ( 30) hydrogen bonds : bond 0.04972 ( 690) hydrogen bonds : angle 3.57047 ( 2205) SS BOND : bond 0.00366 ( 5) SS BOND : angle 1.20737 ( 10) covalent geometry : bond 0.00266 (14150) covalent geometry : angle 0.49245 (19195) *********************** 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 250 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7867 (ptp90) cc_final: 0.7451 (ptp90) REVERT: A 375 LYS cc_start: 0.7233 (mtpt) cc_final: 0.7002 (ttpt) REVERT: B 148 ARG cc_start: 0.7787 (ptp90) cc_final: 0.7397 (ptp90) REVERT: B 158 MET cc_start: 0.8021 (mmm) cc_final: 0.7780 (mmm) REVERT: B 200 MET cc_start: 0.8335 (mtm) cc_final: 0.8125 (mtm) REVERT: B 265 THR cc_start: 0.7541 (p) cc_final: 0.7255 (p) REVERT: B 308 ARG cc_start: 0.7422 (mtm-85) cc_final: 0.7137 (mtp180) REVERT: B 337 ARG cc_start: 0.7460 (mtm180) cc_final: 0.7205 (mtt90) REVERT: C 185 LYS cc_start: 0.8444 (mttp) cc_final: 0.8195 (mmmm) REVERT: C 457 LYS cc_start: 0.7822 (tttt) cc_final: 0.7567 (tptt) REVERT: D 185 LYS cc_start: 0.8517 (mttp) cc_final: 0.8135 (mtpp) REVERT: D 197 MET cc_start: 0.7335 (mtm) cc_final: 0.7075 (mtt) REVERT: D 203 SER cc_start: 0.8588 (t) cc_final: 0.7819 (p) REVERT: D 457 LYS cc_start: 0.7830 (tttp) cc_final: 0.7530 (tptt) REVERT: E 85 ASP cc_start: 0.7712 (p0) cc_final: 0.7399 (p0) REVERT: E 115 ASP cc_start: 0.8000 (m-30) cc_final: 0.7530 (m-30) REVERT: E 148 ARG cc_start: 0.7717 (ptt-90) cc_final: 0.7465 (ptt-90) REVERT: E 170 ASP cc_start: 0.7907 (t0) cc_final: 0.7188 (p0) REVERT: E 308 ARG cc_start: 0.6686 (mtm180) cc_final: 0.6426 (mtt-85) REVERT: E 335 MET cc_start: 0.5181 (mmm) cc_final: 0.4492 (mmt) outliers start: 47 outliers final: 36 residues processed: 229 average time/residue: 0.3249 time to fit residues: 101.2707 Evaluate side-chains 231 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER 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 173 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 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 E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.142715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.120344 restraints weight = 15239.357| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.99 r_work: 0.3167 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14165 Z= 0.155 Angle : 0.536 6.078 19235 Z= 0.285 Chirality : 0.045 0.264 2210 Planarity : 0.004 0.045 2330 Dihedral : 6.429 85.081 2115 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.64 % Allowed : 9.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.20), residues: 1640 helix: 1.87 (0.21), residues: 600 sheet: 0.82 (0.25), residues: 415 loop : -0.10 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 230 HIS 0.004 0.001 HIS A 280 PHE 0.013 0.001 PHE B 159 TYR 0.022 0.002 TYR E 362 ARG 0.003 0.000 ARG E 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 10) link_NAG-ASN : angle 1.92028 ( 30) hydrogen bonds : bond 0.05664 ( 690) hydrogen bonds : angle 3.69680 ( 2205) SS BOND : bond 0.00522 ( 5) SS BOND : angle 1.85999 ( 10) covalent geometry : bond 0.00364 (14150) covalent geometry : angle 0.52991 (19195) *********************** 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 247 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7909 (ptp90) cc_final: 0.7484 (ptp90) REVERT: A 278 ARG cc_start: 0.8180 (mtp180) cc_final: 0.7965 (mtp-110) REVERT: A 375 LYS cc_start: 0.7209 (mtpt) cc_final: 0.7002 (ttpt) REVERT: B 148 ARG cc_start: 0.7864 (ptp90) cc_final: 0.7467 (ptp90) REVERT: B 200 MET cc_start: 0.8480 (mtm) cc_final: 0.8238 (mtm) REVERT: B 265 THR cc_start: 0.7713 (p) cc_final: 0.7444 (p) REVERT: B 308 ARG cc_start: 0.7366 (mtm-85) cc_final: 0.7072 (mtp180) REVERT: C 148 ARG cc_start: 0.8023 (ptt-90) cc_final: 0.7787 (ptt-90) REVERT: C 215 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8465 (mt-10) REVERT: C 265 THR cc_start: 0.7656 (p) cc_final: 0.7420 (p) REVERT: D 197 MET cc_start: 0.7575 (mtm) cc_final: 0.7283 (mtt) REVERT: D 203 SER cc_start: 0.8728 (t) cc_final: 0.7924 (p) REVERT: E 85 ASP cc_start: 0.7824 (p0) cc_final: 0.7556 (p0) REVERT: E 115 ASP cc_start: 0.8002 (m-30) cc_final: 0.7552 (m-30) REVERT: E 148 ARG cc_start: 0.7855 (ptt-90) cc_final: 0.7624 (ptt-90) REVERT: E 170 ASP cc_start: 0.7940 (t0) cc_final: 0.7421 (p0) REVERT: E 235 ASP cc_start: 0.7481 (m-30) cc_final: 0.6844 (t0) REVERT: E 298 LEU cc_start: 0.8015 (mt) cc_final: 0.7624 (tt) REVERT: E 308 ARG cc_start: 0.6889 (mtm180) cc_final: 0.6661 (mtt-85) outliers start: 54 outliers final: 43 residues processed: 224 average time/residue: 0.3402 time to fit residues: 103.5191 Evaluate side-chains 235 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 173 THR Chi-restraints excluded: chain C residue 176 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 263 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 263 SER 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 114 VAL Chi-restraints excluded: chain E residue 142 SER 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 371 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 154 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 34 optimal weight: 0.0170 chunk 18 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.146298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.123454 restraints weight = 15299.963| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.04 r_work: 0.3204 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14165 Z= 0.110 Angle : 0.476 5.542 19235 Z= 0.253 Chirality : 0.042 0.234 2210 Planarity : 0.004 0.046 2330 Dihedral : 5.985 81.252 2115 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.69 % Allowed : 10.51 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1640 helix: 2.06 (0.21), residues: 600 sheet: 0.76 (0.25), residues: 415 loop : -0.04 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 128 HIS 0.003 0.001 HIS C 280 PHE 0.011 0.001 PHE B 282 TYR 0.017 0.001 TYR E 362 ARG 0.003 0.000 ARG E 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 10) link_NAG-ASN : angle 1.50646 ( 30) hydrogen bonds : bond 0.04655 ( 690) hydrogen bonds : angle 3.51919 ( 2205) SS BOND : bond 0.00400 ( 5) SS BOND : angle 1.48418 ( 10) covalent geometry : bond 0.00242 (14150) covalent geometry : angle 0.47180 (19195) *********************** 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 246 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8301 (mp0) cc_final: 0.8038 (mp0) REVERT: A 148 ARG cc_start: 0.7852 (ptp90) cc_final: 0.7446 (ptp90) REVERT: A 278 ARG cc_start: 0.8139 (mtp180) cc_final: 0.7888 (mtp-110) REVERT: A 375 LYS cc_start: 0.7037 (mtpt) cc_final: 0.6836 (ttpt) REVERT: B 148 ARG cc_start: 0.7767 (ptp90) cc_final: 0.7395 (ptp90) REVERT: B 200 MET cc_start: 0.8359 (mtm) cc_final: 0.8156 (mtm) REVERT: B 265 THR cc_start: 0.7531 (p) cc_final: 0.7264 (p) REVERT: B 308 ARG cc_start: 0.7461 (mtm-85) cc_final: 0.7172 (mtp180) REVERT: B 335 MET cc_start: 0.5874 (tpt) cc_final: 0.5232 (tmm) REVERT: C 164 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8664 (mtpp) REVERT: C 185 LYS cc_start: 0.8465 (mttp) cc_final: 0.8235 (mmmm) REVERT: C 265 THR cc_start: 0.7517 (p) cc_final: 0.7299 (p) REVERT: C 457 LYS cc_start: 0.7897 (tttt) cc_final: 0.7568 (tptt) REVERT: D 185 LYS cc_start: 0.8490 (mttp) cc_final: 0.8090 (mtpp) REVERT: D 203 SER cc_start: 0.8721 (t) cc_final: 0.7906 (p) REVERT: D 284 PHE cc_start: 0.7539 (m-80) cc_final: 0.7232 (m-80) REVERT: D 457 LYS cc_start: 0.7946 (tttp) cc_final: 0.7644 (tptt) REVERT: E 115 ASP cc_start: 0.7820 (m-30) cc_final: 0.7379 (m-30) REVERT: E 170 ASP cc_start: 0.7839 (t0) cc_final: 0.7565 (p0) REVERT: E 235 ASP cc_start: 0.7534 (m-30) cc_final: 0.6938 (t0) REVERT: E 298 LEU cc_start: 0.7934 (mt) cc_final: 0.7610 (tt) REVERT: E 308 ARG cc_start: 0.6879 (mtm180) cc_final: 0.6606 (mtt-85) REVERT: E 335 MET cc_start: 0.5191 (tpt) cc_final: 0.4821 (tmm) outliers start: 40 outliers final: 34 residues processed: 233 average time/residue: 0.3259 time to fit residues: 103.5669 Evaluate side-chains 231 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 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 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 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 143 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 144 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 = 0.3556 r_free = 0.3556 target = 0.144413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.122009 restraints weight = 15326.519| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.99 r_work: 0.3192 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4767 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= 0.130 Angle : 0.504 5.324 19235 Z= 0.267 Chirality : 0.043 0.226 2210 Planarity : 0.004 0.046 2330 Dihedral : 5.725 74.473 2115 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.96 % Allowed : 10.64 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1640 helix: 2.03 (0.21), residues: 600 sheet: 0.70 (0.25), residues: 415 loop : -0.11 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 128 HIS 0.004 0.001 HIS C 280 PHE 0.012 0.001 PHE E 205 TYR 0.020 0.001 TYR E 362 ARG 0.005 0.000 ARG C 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 10) link_NAG-ASN : angle 1.77850 ( 30) hydrogen bonds : bond 0.05009 ( 690) hydrogen bonds : angle 3.53592 ( 2205) SS BOND : bond 0.00431 ( 5) SS BOND : angle 1.49086 ( 10) covalent geometry : bond 0.00300 (14150) covalent geometry : angle 0.49848 (19195) *********************** 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 248 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7867 (ptp90) cc_final: 0.7466 (ptp90) REVERT: B 113 GLU cc_start: 0.8003 (mp0) cc_final: 0.7759 (mp0) REVERT: B 148 ARG cc_start: 0.7812 (ptp90) cc_final: 0.7439 (ptp90) REVERT: B 265 THR cc_start: 0.7578 (p) cc_final: 0.7310 (p) REVERT: B 308 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.7152 (mtp180) REVERT: B 335 MET cc_start: 0.5920 (tpt) cc_final: 0.5387 (tmm) REVERT: C 164 LYS cc_start: 0.8908 (mtpp) cc_final: 0.8659 (mtpp) REVERT: C 185 LYS cc_start: 0.8488 (mttp) cc_final: 0.8254 (mmmm) REVERT: C 265 THR cc_start: 0.7617 (p) cc_final: 0.7377 (p) REVERT: C 457 LYS cc_start: 0.7980 (tttt) cc_final: 0.7297 (ttpp) REVERT: D 185 LYS cc_start: 0.8541 (mttp) cc_final: 0.8134 (mtpp) REVERT: D 203 SER cc_start: 0.8745 (t) cc_final: 0.7968 (p) REVERT: D 337 ARG cc_start: 0.7211 (mtm180) cc_final: 0.6515 (mpt-90) REVERT: D 457 LYS cc_start: 0.8009 (tttp) cc_final: 0.7695 (tptt) REVERT: E 140 ASN cc_start: 0.7616 (t0) cc_final: 0.7390 (t0) REVERT: E 143 MET cc_start: 0.7778 (mmt) cc_final: 0.7340 (mmt) REVERT: E 148 ARG cc_start: 0.7749 (ptt-90) cc_final: 0.7477 (ptt-90) REVERT: E 235 ASP cc_start: 0.7637 (m-30) cc_final: 0.7027 (t0) REVERT: E 298 LEU cc_start: 0.7960 (mt) cc_final: 0.7633 (tt) REVERT: E 308 ARG cc_start: 0.6886 (mtm180) cc_final: 0.6625 (mtt-85) outliers start: 44 outliers final: 39 residues processed: 233 average time/residue: 0.3305 time to fit residues: 104.2574 Evaluate side-chains 242 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.144549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.122246 restraints weight = 15275.844| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.97 r_work: 0.3194 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14165 Z= 0.129 Angle : 0.507 6.318 19235 Z= 0.268 Chirality : 0.043 0.216 2210 Planarity : 0.004 0.043 2330 Dihedral : 5.450 65.304 2115 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.83 % Allowed : 10.91 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1640 helix: 2.04 (0.21), residues: 600 sheet: 0.65 (0.25), residues: 415 loop : -0.12 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 128 HIS 0.004 0.001 HIS E 169 PHE 0.011 0.001 PHE E 205 TYR 0.018 0.001 TYR E 362 ARG 0.006 0.000 ARG C 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 10) link_NAG-ASN : angle 1.97187 ( 30) hydrogen bonds : bond 0.04920 ( 690) hydrogen bonds : angle 3.53847 ( 2205) SS BOND : bond 0.00446 ( 5) SS BOND : angle 1.39646 ( 10) covalent geometry : bond 0.00297 (14150) covalent geometry : angle 0.50024 (19195) *********************** 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 244 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8140 (mp0) cc_final: 0.7895 (mp0) REVERT: A 148 ARG cc_start: 0.7879 (ptp90) cc_final: 0.7481 (ptp90) REVERT: B 148 ARG cc_start: 0.7792 (ptp90) cc_final: 0.7429 (ptp90) REVERT: B 265 THR cc_start: 0.7607 (p) cc_final: 0.7345 (p) REVERT: B 308 ARG cc_start: 0.7448 (mtm-85) cc_final: 0.7153 (mtp180) REVERT: C 148 ARG cc_start: 0.7892 (ptt-90) cc_final: 0.7604 (ptt-90) REVERT: C 164 LYS cc_start: 0.8919 (mtpp) cc_final: 0.8677 (mtpp) REVERT: C 185 LYS cc_start: 0.8495 (mttp) cc_final: 0.8260 (mmmm) REVERT: C 265 THR cc_start: 0.7543 (p) cc_final: 0.7317 (p) REVERT: C 457 LYS cc_start: 0.8000 (tttt) cc_final: 0.7318 (ttpp) REVERT: D 158 MET cc_start: 0.8017 (mmm) cc_final: 0.7792 (mmm) REVERT: D 185 LYS cc_start: 0.8547 (mttp) cc_final: 0.8129 (mtpp) REVERT: D 203 SER cc_start: 0.8721 (t) cc_final: 0.7956 (p) REVERT: D 337 ARG cc_start: 0.7258 (mtm180) cc_final: 0.6555 (mpt-90) REVERT: D 457 LYS cc_start: 0.8037 (tttp) cc_final: 0.7726 (tptt) REVERT: E 140 ASN cc_start: 0.7650 (t0) cc_final: 0.7406 (t0) REVERT: E 148 ARG cc_start: 0.7779 (ptt-90) cc_final: 0.7472 (ptt-90) REVERT: E 235 ASP cc_start: 0.7701 (m-30) cc_final: 0.7068 (t0) REVERT: E 298 LEU cc_start: 0.7928 (mt) cc_final: 0.7621 (tt) REVERT: E 308 ARG cc_start: 0.6931 (mtm180) cc_final: 0.6670 (mtt-85) REVERT: E 335 MET cc_start: 0.5441 (tpt) cc_final: 0.4848 (tmm) outliers start: 42 outliers final: 41 residues processed: 232 average time/residue: 0.3277 time to fit residues: 103.4224 Evaluate side-chains 240 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 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 114 VAL Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 115 optimal weight: 0.0670 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.141976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120018 restraints weight = 15590.557| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.97 r_work: 0.3161 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4956 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= 0.139 Angle : 0.517 5.819 19235 Z= 0.274 Chirality : 0.043 0.209 2210 Planarity : 0.004 0.041 2330 Dihedral : 5.196 52.807 2115 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.90 % Allowed : 11.04 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1640 helix: 2.01 (0.21), residues: 600 sheet: 0.61 (0.25), residues: 415 loop : -0.17 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 128 HIS 0.004 0.001 HIS C 280 PHE 0.012 0.001 PHE E 205 TYR 0.019 0.001 TYR E 362 ARG 0.006 0.000 ARG C 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 10) link_NAG-ASN : angle 1.67495 ( 30) hydrogen bonds : bond 0.05118 ( 690) hydrogen bonds : angle 3.58101 ( 2205) SS BOND : bond 0.00464 ( 5) SS BOND : angle 1.50456 ( 10) covalent geometry : bond 0.00325 (14150) covalent geometry : angle 0.51169 (19195) *********************** 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 255 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 212 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7762 (ptp90) cc_final: 0.7333 (ptp90) REVERT: A 263 SER cc_start: 0.8663 (t) cc_final: 0.8444 (m) REVERT: A 278 ARG cc_start: 0.8049 (mtp180) cc_final: 0.7727 (mtp-110) REVERT: B 148 ARG cc_start: 0.7604 (ptp90) cc_final: 0.7239 (ptp90) REVERT: B 201 ASP cc_start: 0.7558 (t70) cc_final: 0.7229 (t70) REVERT: B 265 THR cc_start: 0.7411 (p) cc_final: 0.7130 (p) REVERT: B 308 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.7088 (mtp180) REVERT: B 335 MET cc_start: 0.5913 (tpt) cc_final: 0.5099 (tmm) REVERT: C 115 ASP cc_start: 0.7356 (m-30) cc_final: 0.7049 (m-30) REVERT: C 164 LYS cc_start: 0.8795 (mtpp) cc_final: 0.8510 (mtpp) REVERT: C 265 THR cc_start: 0.7330 (p) cc_final: 0.7068 (p) REVERT: C 337 ARG cc_start: 0.7257 (mtm180) cc_final: 0.6516 (mpt-90) REVERT: D 158 MET cc_start: 0.7960 (mmm) cc_final: 0.7701 (mmm) REVERT: D 185 LYS cc_start: 0.8266 (mttp) cc_final: 0.7774 (mtpp) REVERT: D 203 SER cc_start: 0.8557 (t) cc_final: 0.7732 (p) REVERT: D 337 ARG cc_start: 0.7039 (mtm180) cc_final: 0.6685 (mtt180) REVERT: D 457 LYS cc_start: 0.7800 (tttp) cc_final: 0.7476 (tptt) REVERT: E 148 ARG cc_start: 0.7621 (ptt-90) cc_final: 0.7289 (ptt-90) REVERT: E 235 ASP cc_start: 0.7658 (m-30) cc_final: 0.6844 (t0) REVERT: E 298 LEU cc_start: 0.7610 (mt) cc_final: 0.7271 (tt) REVERT: E 308 ARG cc_start: 0.6911 (mtm180) cc_final: 0.6642 (mtt-85) REVERT: E 335 MET cc_start: 0.5427 (tpt) cc_final: 0.4860 (tmm) REVERT: E 375 LYS cc_start: 0.6792 (mtpt) cc_final: 0.6574 (ttpt) outliers start: 43 outliers final: 41 residues processed: 242 average time/residue: 0.3172 time to fit residues: 104.3009 Evaluate side-chains 247 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 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 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 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 145 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 48 optimal weight: 0.0570 chunk 65 optimal weight: 2.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.144830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.121920 restraints weight = 15430.028| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.06 r_work: 0.3179 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14165 Z= 0.122 Angle : 0.508 7.674 19235 Z= 0.268 Chirality : 0.043 0.200 2210 Planarity : 0.004 0.040 2330 Dihedral : 5.083 44.025 2115 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.69 % Allowed : 11.25 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1640 helix: 2.09 (0.21), residues: 600 sheet: 0.63 (0.25), residues: 415 loop : -0.14 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.003 0.001 HIS C 280 PHE 0.012 0.001 PHE B 282 TYR 0.017 0.001 TYR E 362 ARG 0.008 0.000 ARG C 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 10) link_NAG-ASN : angle 2.12843 ( 30) hydrogen bonds : bond 0.04739 ( 690) hydrogen bonds : angle 3.51671 ( 2205) SS BOND : bond 0.00409 ( 5) SS BOND : angle 1.32762 ( 10) covalent geometry : bond 0.00274 (14150) covalent geometry : angle 0.50023 (19195) ********************** 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 245 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7894 (ptp90) cc_final: 0.7514 (ptp90) REVERT: A 263 SER cc_start: 0.8717 (t) cc_final: 0.8515 (m) REVERT: B 148 ARG cc_start: 0.7676 (ptp90) cc_final: 0.7317 (ptp90) REVERT: B 201 ASP cc_start: 0.7651 (t70) cc_final: 0.7380 (t70) REVERT: B 265 THR cc_start: 0.7578 (p) cc_final: 0.7313 (p) REVERT: B 308 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.7142 (mtp180) REVERT: B 335 MET cc_start: 0.5906 (tpt) cc_final: 0.5172 (tmm) REVERT: C 115 ASP cc_start: 0.7620 (m-30) cc_final: 0.7322 (m-30) REVERT: C 148 ARG cc_start: 0.7920 (ptt-90) cc_final: 0.7711 (ptt-90) REVERT: C 164 LYS cc_start: 0.8915 (mtpp) cc_final: 0.8684 (mtpp) REVERT: C 185 LYS cc_start: 0.8508 (mttp) cc_final: 0.8123 (mtmt) REVERT: C 265 THR cc_start: 0.7503 (p) cc_final: 0.7263 (p) REVERT: C 337 ARG cc_start: 0.7434 (mtm180) cc_final: 0.6791 (mpt-90) REVERT: C 457 LYS cc_start: 0.8005 (tttt) cc_final: 0.7308 (ttpp) REVERT: D 158 MET cc_start: 0.8060 (mmm) cc_final: 0.7832 (mmm) REVERT: D 185 LYS cc_start: 0.8555 (mttp) cc_final: 0.8109 (mtpp) REVERT: D 203 SER cc_start: 0.8728 (t) cc_final: 0.7962 (p) REVERT: D 337 ARG cc_start: 0.7342 (mtm180) cc_final: 0.7034 (mtt180) REVERT: D 457 LYS cc_start: 0.8003 (tttp) cc_final: 0.7689 (tptt) REVERT: E 148 ARG cc_start: 0.7751 (ptt-90) cc_final: 0.7455 (ptt-90) REVERT: E 235 ASP cc_start: 0.7823 (m-30) cc_final: 0.7039 (t0) REVERT: E 298 LEU cc_start: 0.7939 (mt) cc_final: 0.7696 (tt) REVERT: E 308 ARG cc_start: 0.6935 (mtm180) cc_final: 0.6679 (mtt-85) REVERT: E 335 MET cc_start: 0.5557 (tpt) cc_final: 0.5005 (tmm) REVERT: E 375 LYS cc_start: 0.7075 (mtpt) cc_final: 0.6833 (ttpt) outliers start: 40 outliers final: 39 residues processed: 233 average time/residue: 0.3510 time to fit residues: 111.4449 Evaluate side-chains 244 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 145 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.144805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.121748 restraints weight = 15562.401| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.08 r_work: 0.3180 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14165 Z= 0.121 Angle : 0.520 8.415 19235 Z= 0.270 Chirality : 0.043 0.206 2210 Planarity : 0.004 0.039 2330 Dihedral : 4.951 43.886 2115 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.76 % Allowed : 11.25 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1640 helix: 2.10 (0.21), residues: 600 sheet: 0.61 (0.25), residues: 415 loop : -0.14 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 128 HIS 0.003 0.001 HIS C 280 PHE 0.012 0.001 PHE B 282 TYR 0.018 0.001 TYR E 362 ARG 0.006 0.000 ARG C 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 10) link_NAG-ASN : angle 2.34727 ( 30) hydrogen bonds : bond 0.04714 ( 690) hydrogen bonds : angle 3.50414 ( 2205) SS BOND : bond 0.00417 ( 5) SS BOND : angle 1.31863 ( 10) covalent geometry : bond 0.00276 (14150) covalent geometry : angle 0.51134 (19195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6677.57 seconds wall clock time: 116 minutes 58.16 seconds (7018.16 seconds total)