Starting phenix.real_space_refine on Fri May 16 17:02:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oq8_17108/05_2025/8oq8_17108.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oq8_17108/05_2025/8oq8_17108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oq8_17108/05_2025/8oq8_17108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oq8_17108/05_2025/8oq8_17108.map" model { file = "/net/cci-nas-00/data/ceres_data/8oq8_17108/05_2025/8oq8_17108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oq8_17108/05_2025/8oq8_17108.cif" } resolution = 2.9 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: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 9428 2.51 5 N 2248 2.21 5 O 2681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14432 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2765 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2757 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2768 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2761 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2778 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 111 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2, 'RI5': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, '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: "C" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, '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: "D" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, '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: "E" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, '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: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 9.82, per 1000 atoms: 0.68 Number of scatterers: 14432 At special positions: 0 Unit cell: (93.4775, 95.495, 140.553, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 2681 8.00 N 2248 7.00 C 9428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM13855 O5 NAG A 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14142 O5 NAG D 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14052 O5 NAG C 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14232 O5 NAG E 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM13841 O5 NAG A 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM13962 O5 NAG B 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14066 O5 NAG C 503 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 140 " " NAG A 502 " - " ASN A 234 " " NAG B 502 " - " ASN B 140 " " NAG B 503 " - " ASN B 234 " " NAG C 502 " - " ASN C 140 " " NAG C 503 " - " ASN C 234 " " NAG D 502 " - " ASN D 140 " " NAG D 503 " - " ASN D 234 " " NAG E 502 " - " ASN E 140 " " NAG E 503 " - " ASN E 234 " Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 1.7 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 40.6% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 146 through 153 removed outlier: 3.973A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 153 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 280 through 299 removed outlier: 3.839A pdb=" N PHE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 309 through 334 Proline residue: A 315 - end of helix removed outlier: 3.511A pdb=" N SER A 334 " --> pdb=" O GLY A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 380 removed outlier: 3.568A pdb=" N ILE A 346 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 478 removed outlier: 3.999A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'B' and resid 74 through 78 Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.613A pdb=" N ILE B 153 " --> pdb=" O VAL B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 280 through 300 removed outlier: 3.822A pdb=" N PHE B 284 " --> pdb=" O HIS B 280 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.641A pdb=" N TRP B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 309 through 335 Proline residue: B 315 - end of helix removed outlier: 3.630A pdb=" N SER B 334 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 380 removed outlier: 3.687A pdb=" N ILE B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 478 removed outlier: 3.926A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.722A pdb=" N HIS C 84 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 134 Processing helix chain 'C' and resid 146 through 153 removed outlier: 4.322A 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 280 through 300 removed outlier: 3.835A pdb=" N PHE C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.693A pdb=" N TRP C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 309 through 335 Proline residue: C 315 - end of helix removed outlier: 3.597A pdb=" N MET C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 380 removed outlier: 3.576A pdb=" N ILE C 346 " --> pdb=" O LYS C 342 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 360 " --> pdb=" O PHE C 356 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 478 removed outlier: 4.039A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Proline residue: C 464 - end of helix Processing helix chain 'D' and resid 74 through 78 Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 232 through 235 Processing helix chain 'D' and resid 280 through 300 removed outlier: 3.826A pdb=" N PHE D 284 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.644A pdb=" N TRP D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 309 through 333 Proline residue: D 315 - end of helix Processing helix chain 'D' and resid 342 through 380 removed outlier: 3.543A pdb=" N ILE D 346 " --> pdb=" O LYS D 342 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR D 347 " --> pdb=" O ALA D 343 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 360 " --> pdb=" O PHE D 356 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 478 removed outlier: 3.917A pdb=" N ILE D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Proline residue: D 464 - end of helix Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.549A pdb=" N ILE E 153 " --> pdb=" O VAL E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 280 through 300 removed outlier: 3.878A pdb=" N PHE E 284 " --> pdb=" O HIS E 280 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.712A pdb=" N TRP E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 309 through 334 Proline residue: E 315 - end of helix removed outlier: 3.644A pdb=" N SER E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 380 removed outlier: 3.663A pdb=" N ILE E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR E 347 " --> pdb=" O ALA E 343 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 360 " --> pdb=" O PHE E 356 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR E 362 " --> pdb=" O SER E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 478 removed outlier: 3.966A pdb=" N ILE E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 145 removed outlier: 7.334A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 removed outlier: 6.911A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE A 168 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ARG A 191 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.237A 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: 4.732A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N SER A 218 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASN A 269 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 256 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR A 276 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLU A 252 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ARG A 278 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE A 250 " --> pdb=" O ARG A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 145 removed outlier: 7.389A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 168 removed outlier: 6.906A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE B 168 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ARG B 191 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.207A 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: 4.704A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER B 218 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASN B 269 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR B 276 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU B 252 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG B 278 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ILE B 250 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.878A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR C 121 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU C 108 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N TYR C 123 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLU C 106 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ARG C 125 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLN C 104 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N TYR C 127 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ASP C 102 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N LYS C 129 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N GLY C 100 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 163 through 168 removed outlier: 6.851A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE C 168 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ARG C 191 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR C 121 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU C 108 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N TYR C 123 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLU C 106 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ARG C 125 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLN C 104 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N TYR C 127 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ASP C 102 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N LYS C 129 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N GLY C 100 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.692A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER C 218 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN C 269 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR C 276 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLU C 252 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ARG C 278 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE C 250 " --> pdb=" O ARG C 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 143 through 145 removed outlier: 3.836A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR D 121 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU D 108 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N TYR D 123 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLU D 106 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ARG D 125 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLN D 104 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR D 127 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASP D 102 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N LYS D 129 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N GLY D 100 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 163 through 168 removed outlier: 6.873A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE D 168 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ARG D 191 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR D 121 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU D 108 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N TYR D 123 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLU D 106 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ARG D 125 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLN D 104 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR D 127 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASP D 102 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N LYS D 129 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N GLY D 100 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.734A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N SER D 218 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASN D 269 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR D 276 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU D 252 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ARG D 278 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE D 250 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 145 removed outlier: 3.963A pdb=" N SER E 110 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR E 121 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU E 108 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N TYR E 123 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLU E 106 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ARG E 125 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLN E 104 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N TYR E 127 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASP E 102 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N LYS E 129 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N GLY E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.840A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE E 168 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ARG E 191 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER E 110 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR E 121 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU E 108 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N TYR E 123 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLU E 106 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ARG E 125 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLN E 104 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N TYR E 127 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASP E 102 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N LYS E 129 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N GLY E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.679A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER E 218 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN E 269 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR E 276 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLU E 252 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG E 278 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE E 250 " --> pdb=" O ARG E 278 " (cutoff:3.500A) 772 hydrogen bonds defined for protein. 2130 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: 4.49 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2350 1.32 - 1.44: 4148 1.44 - 1.57: 8005 1.57 - 1.69: 1 1.69 - 1.81: 140 Bond restraints: 14644 Sorted by residual: bond pdb=" CG1 ILE E 111 " pdb=" CD1 ILE E 111 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.45e+00 bond pdb=" CB ASP D 102 " pdb=" CG ASP D 102 " ideal model delta sigma weight residual 1.516 1.458 0.058 2.50e-02 1.60e+03 5.36e+00 bond pdb=" C15 RI5 A 510 " pdb=" O16 RI5 A 510 " ideal model delta sigma weight residual 1.396 1.442 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" CG1 ILE D 111 " pdb=" CD1 ILE D 111 " ideal model delta sigma weight residual 1.513 1.424 0.089 3.90e-02 6.57e+02 5.22e+00 bond pdb=" CB PRO D 206 " pdb=" CG PRO D 206 " ideal model delta sigma weight residual 1.506 1.422 0.084 3.90e-02 6.57e+02 4.69e+00 ... (remaining 14639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 18585 1.85 - 3.71: 1000 3.71 - 5.56: 184 5.56 - 7.41: 11 7.41 - 9.26: 3 Bond angle restraints: 19783 Sorted by residual: angle pdb=" N GLU C 252 " pdb=" CA GLU C 252 " pdb=" C GLU C 252 " ideal model delta sigma weight residual 110.91 114.52 -3.61 1.17e+00 7.31e-01 9.53e+00 angle pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " pdb=" CG LEU B 190 " ideal model delta sigma weight residual 116.30 125.56 -9.26 3.50e+00 8.16e-02 7.01e+00 angle pdb=" CA LEU C 190 " pdb=" CB LEU C 190 " pdb=" CG LEU C 190 " ideal model delta sigma weight residual 116.30 125.50 -9.20 3.50e+00 8.16e-02 6.92e+00 angle pdb=" CA TYR A 340 " pdb=" CB TYR A 340 " pdb=" CG TYR A 340 " ideal model delta sigma weight residual 113.90 118.48 -4.58 1.80e+00 3.09e-01 6.48e+00 angle pdb=" N THR B 265 " pdb=" CA THR B 265 " pdb=" C THR B 265 " ideal model delta sigma weight residual 110.80 116.15 -5.35 2.13e+00 2.20e-01 6.31e+00 ... (remaining 19778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8336 17.79 - 35.57: 376 35.57 - 53.36: 73 53.36 - 71.14: 22 71.14 - 88.93: 2 Dihedral angle restraints: 8809 sinusoidal: 3794 harmonic: 5015 Sorted by residual: dihedral pdb=" CA SER C 339 " pdb=" C SER C 339 " pdb=" N TYR C 340 " pdb=" CA TYR C 340 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA SER B 339 " pdb=" C SER B 339 " pdb=" N TYR B 340 " pdb=" CA TYR B 340 " ideal model delta harmonic sigma weight residual 180.00 161.94 18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA SER D 339 " pdb=" C SER D 339 " pdb=" N TYR D 340 " pdb=" CA TYR D 340 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 8806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 2233 0.287 - 0.574: 3 0.574 - 0.860: 0 0.860 - 1.147: 1 1.147 - 1.434: 2 Chirality restraints: 2239 Sorted by residual: chirality pdb=" C1 NAG B 503 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B 503 " pdb=" O5 NAG B 503 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-01 2.50e+01 5.14e+01 chirality pdb=" C1 NAG C 503 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 503 " pdb=" O5 NAG C 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.07 -1.33 2.00e-01 2.50e+01 4.40e+01 chirality pdb=" C1 NAG E 503 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 503 " pdb=" O5 NAG E 503 " both_signs ideal model delta sigma weight residual False -2.40 -3.36 0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 2236 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " 0.361 2.00e-02 2.50e+03 3.77e-01 1.78e+03 pdb=" CG ASN E 234 " -0.129 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " -0.123 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " -0.576 2.00e-02 2.50e+03 pdb=" C1 NAG E 503 " 0.466 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.296 2.00e-02 2.50e+03 3.73e-01 1.74e+03 pdb=" CG ASN D 234 " -0.133 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.580 2.00e-02 2.50e+03 pdb=" C1 NAG D 503 " 0.496 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.171 2.00e-02 2.50e+03 3.32e-01 1.38e+03 pdb=" CG ASN A 234 " 0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.087 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.571 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " -0.421 2.00e-02 2.50e+03 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 824 2.72 - 3.26: 12573 3.26 - 3.81: 21068 3.81 - 4.35: 27850 4.35 - 4.90: 49226 Nonbonded interactions: 111541 Sorted by model distance: nonbonded pdb=" OD1 ASN C 269 " pdb=" O HOH C 601 " model vdw 2.175 3.040 nonbonded pdb=" OD1 ASN D 269 " pdb=" O HOH D 601 " model vdw 2.194 3.040 nonbonded pdb=" O HOH A 605 " pdb=" O HOH A 620 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP E 115 " pdb=" O HOH E 601 " model vdw 2.250 3.040 nonbonded pdb=" O ASP C 174 " pdb=" O HOH C 602 " model vdw 2.286 3.040 ... (remaining 111536 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 74 through 372 or (resid 373 through 374 and (name N or na \ me CA or name C or name O or name CB )) or resid 375 or (resid 376 through 380 a \ nd (name N or name CA or name C or name O or name CB )) or resid 451 through 479 \ or resid 502 or resid 504 through 505)) selection = (chain 'B' and (resid 74 through 372 or (resid 373 through 374 and (name N or na \ me CA or name C or name O or name CB )) or resid 375 through 479 or resid 502 or \ resid 504 through 505)) selection = (chain 'C' and (resid 74 through 372 or (resid 373 through 374 and (name N or na \ me CA or name C or name O or name CB )) or resid 375 or (resid 376 through 380 a \ nd (name N or name CA or name C or name O or name CB )) or resid 451 through 479 \ or resid 502 or resid 504 through 505)) selection = (chain 'D' and (resid 74 through 373 or (resid 374 and (name N or name CA or nam \ e C or name O or name CB )) or resid 375 or (resid 376 through 380 and (name N o \ r name CA or name C or name O or name CB )) or resid 451 through 479 or resid 50 \ 2 or resid 504 through 505)) selection = (chain 'E' and (resid 74 through 372 or (resid 373 through 374 and (name N or na \ me CA or name C or name O or name CB )) or resid 375 or (resid 376 through 380 a \ nd (name N or name CA or name C or name O or name CB )) or resid 451 through 479 \ or resid 502 or resid 504 through 505)) } 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.200 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 0.014 0.311 14654 Z= 0.567 Angle : 1.469 50.573 19813 Z= 0.617 Chirality : 0.081 1.434 2239 Planarity : 0.008 0.052 2394 Dihedral : 11.030 88.930 5549 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.84 % Allowed : 2.98 % Favored : 96.18 % 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: 1.82 (0.20), residues: 1660 helix: 1.88 (0.22), residues: 530 sheet: 1.30 (0.23), residues: 440 loop : 0.77 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 300 HIS 0.009 0.003 HIS A 254 PHE 0.024 0.004 PHE B 253 TYR 0.021 0.004 TYR D 219 ARG 0.020 0.003 ARG C 337 Details of bonding type rmsd link_NAG-ASN : bond 0.13151 ( 10) link_NAG-ASN : angle 28.41387 ( 30) hydrogen bonds : bond 0.20742 ( 689) hydrogen bonds : angle 5.77573 ( 2130) covalent geometry : bond 0.01356 (14644) covalent geometry : angle 0.96742 (19783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 290 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7602 (mt) cc_final: 0.7334 (mp) REVERT: A 179 ARG cc_start: 0.8106 (ttp-170) cc_final: 0.7549 (ttm-80) REVERT: A 238 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8054 (mmtp) REVERT: A 269 ASN cc_start: 0.8418 (m-40) cc_final: 0.7562 (t0) REVERT: A 335 MET cc_start: 0.7636 (mtm) cc_final: 0.6924 (mmp) REVERT: A 345 ASP cc_start: 0.8059 (m-30) cc_final: 0.7578 (m-30) REVERT: B 143 MET cc_start: 0.8680 (mtm) cc_final: 0.8432 (mtp) REVERT: B 151 LYS cc_start: 0.8368 (mmtt) cc_final: 0.7865 (mptt) REVERT: B 235 ASP cc_start: 0.7904 (m-30) cc_final: 0.7676 (m-30) REVERT: B 269 ASN cc_start: 0.8360 (m-40) cc_final: 0.7990 (m-40) REVERT: B 308 ARG cc_start: 0.7422 (mtm180) cc_final: 0.7141 (mtm110) REVERT: C 82 ASP cc_start: 0.7457 (m-30) cc_final: 0.6129 (p0) REVERT: C 92 PHE cc_start: 0.8223 (t80) cc_final: 0.7874 (t80) REVERT: C 116 MET cc_start: 0.8704 (mtm) cc_final: 0.8372 (mtp) REVERT: C 151 LYS cc_start: 0.8390 (mmtt) cc_final: 0.8064 (mmtp) REVERT: C 179 ARG cc_start: 0.7947 (ttp-170) cc_final: 0.7677 (ttp-170) REVERT: C 269 ASN cc_start: 0.8263 (m-40) cc_final: 0.8015 (t0) REVERT: D 114 VAL cc_start: 0.7958 (t) cc_final: 0.7581 (p) REVERT: D 179 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7592 (ttp-170) REVERT: E 106 GLU cc_start: 0.7373 (tt0) cc_final: 0.6809 (tt0) REVERT: E 116 MET cc_start: 0.8779 (mtm) cc_final: 0.8515 (mtp) REVERT: E 232 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7553 (mmtt) REVERT: E 269 ASN cc_start: 0.8679 (m-40) cc_final: 0.8173 (m-40) REVERT: E 372 GLN cc_start: 0.7789 (tp40) cc_final: 0.7474 (mm-40) outliers start: 13 outliers final: 8 residues processed: 301 average time/residue: 1.5075 time to fit residues: 489.7049 Evaluate side-chains 242 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 234 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 461 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 149 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 269 ASN A 287 GLN C 251 GLN C 287 GLN C 372 GLN D 162 HIS D 251 GLN E 247 GLN E 251 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.120976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.095103 restraints weight = 16564.770| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.86 r_work: 0.2747 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14654 Z= 0.143 Angle : 0.607 23.443 19813 Z= 0.306 Chirality : 0.045 0.661 2239 Planarity : 0.004 0.034 2394 Dihedral : 8.353 59.863 2346 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.13 % Allowed : 9.25 % Favored : 88.62 % 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: 2.00 (0.21), residues: 1660 helix: 2.50 (0.23), residues: 530 sheet: 1.07 (0.24), residues: 465 loop : 0.67 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 128 HIS 0.004 0.001 HIS C 254 PHE 0.015 0.001 PHE B 92 TYR 0.021 0.002 TYR E 272 ARG 0.007 0.000 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00636 ( 10) link_NAG-ASN : angle 6.64584 ( 30) hydrogen bonds : bond 0.07206 ( 689) hydrogen bonds : angle 4.23896 ( 2130) covalent geometry : bond 0.00258 (14644) covalent geometry : angle 0.54972 (19783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 1.628 Fit side-chains REVERT: A 179 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.7468 (ttm-80) REVERT: A 269 ASN cc_start: 0.8537 (m110) cc_final: 0.8219 (m-40) REVERT: A 335 MET cc_start: 0.7834 (mtm) cc_final: 0.6829 (mmp) REVERT: A 345 ASP cc_start: 0.8296 (m-30) cc_final: 0.7903 (m-30) REVERT: B 151 LYS cc_start: 0.8506 (mmtt) cc_final: 0.7897 (mptt) REVERT: B 241 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6635 (mm-30) REVERT: B 278 ARG cc_start: 0.8226 (mtt-85) cc_final: 0.7995 (mtp85) REVERT: B 308 ARG cc_start: 0.7682 (mtm180) cc_final: 0.7366 (mtm110) REVERT: C 82 ASP cc_start: 0.7445 (m-30) cc_final: 0.6089 (p0) REVERT: C 116 MET cc_start: 0.8650 (mtm) cc_final: 0.8104 (mtp) REVERT: C 151 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8143 (mmtp) REVERT: C 179 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.7920 (ttm-80) REVERT: C 235 ASP cc_start: 0.8249 (m-30) cc_final: 0.7991 (m-30) REVERT: C 242 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6232 (mtt90) REVERT: D 113 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7908 (mt-10) REVERT: D 114 VAL cc_start: 0.7692 (t) cc_final: 0.7400 (p) REVERT: D 179 ARG cc_start: 0.8141 (ttp-170) cc_final: 0.7705 (ttp-170) REVERT: E 106 GLU cc_start: 0.7980 (tt0) cc_final: 0.7441 (tt0) REVERT: E 116 MET cc_start: 0.8699 (mtm) cc_final: 0.8453 (mtp) REVERT: E 232 LYS cc_start: 0.8398 (mtmm) cc_final: 0.7574 (mmpt) REVERT: E 269 ASN cc_start: 0.8690 (m-40) cc_final: 0.8282 (t0) REVERT: E 373 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6617 (tm-30) REVERT: E 375 LYS cc_start: 0.6429 (tmtt) cc_final: 0.6184 (tmtt) outliers start: 33 outliers final: 14 residues processed: 277 average time/residue: 1.4684 time to fit residues: 440.2239 Evaluate side-chains 259 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 244 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 240 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 149 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 138 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 63 optimal weight: 0.0670 chunk 105 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 199 ASN A 287 GLN A 372 GLN C 251 GLN C 287 GLN C 372 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN E 251 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.094136 restraints weight = 16705.303| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.88 r_work: 0.2749 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14654 Z= 0.130 Angle : 0.577 22.128 19813 Z= 0.290 Chirality : 0.043 0.581 2239 Planarity : 0.004 0.038 2394 Dihedral : 7.754 59.397 2338 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.04 % Allowed : 10.54 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.21), residues: 1660 helix: 2.66 (0.24), residues: 530 sheet: 1.09 (0.24), residues: 470 loop : 0.70 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.004 0.001 HIS C 254 PHE 0.015 0.001 PHE B 92 TYR 0.016 0.002 TYR B 272 ARG 0.005 0.000 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00786 ( 10) link_NAG-ASN : angle 6.78388 ( 30) hydrogen bonds : bond 0.06531 ( 689) hydrogen bonds : angle 3.94814 ( 2130) covalent geometry : bond 0.00236 (14644) covalent geometry : angle 0.51375 (19783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8162 (ttp-170) cc_final: 0.7370 (ttm-80) REVERT: A 269 ASN cc_start: 0.8513 (m110) cc_final: 0.8143 (m-40) REVERT: A 335 MET cc_start: 0.7733 (mtm) cc_final: 0.6725 (mmp) REVERT: A 345 ASP cc_start: 0.8242 (m-30) cc_final: 0.7863 (m-30) REVERT: A 372 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7289 (tp-100) REVERT: B 108 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8203 (mp) REVERT: B 151 LYS cc_start: 0.8492 (mmtt) cc_final: 0.7845 (mptt) REVERT: B 232 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7927 (mtmt) REVERT: B 241 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6614 (mm-30) REVERT: B 278 ARG cc_start: 0.8129 (mtt-85) cc_final: 0.7887 (mtp85) REVERT: B 308 ARG cc_start: 0.7652 (mtm180) cc_final: 0.7337 (mtm110) REVERT: C 82 ASP cc_start: 0.7459 (m-30) cc_final: 0.6128 (p0) REVERT: C 116 MET cc_start: 0.8628 (mtm) cc_final: 0.8075 (mtp) REVERT: C 151 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8115 (mmtp) REVERT: C 179 ARG cc_start: 0.8422 (ttp-170) cc_final: 0.7890 (ttm-80) REVERT: C 223 GLU cc_start: 0.7680 (pt0) cc_final: 0.7465 (tp30) REVERT: C 240 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6725 (t70) REVERT: C 242 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6504 (mtt90) REVERT: D 114 VAL cc_start: 0.7636 (t) cc_final: 0.7309 (p) REVERT: D 179 ARG cc_start: 0.8049 (ttp-170) cc_final: 0.7615 (ttp-170) REVERT: E 106 GLU cc_start: 0.7958 (tt0) cc_final: 0.7391 (tt0) REVERT: E 116 MET cc_start: 0.8711 (mtm) cc_final: 0.8471 (mtp) REVERT: E 232 LYS cc_start: 0.8329 (mtmm) cc_final: 0.7516 (mmpt) REVERT: E 269 ASN cc_start: 0.8668 (m-40) cc_final: 0.8228 (t0) REVERT: E 373 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6509 (tm-30) REVERT: E 375 LYS cc_start: 0.6467 (OUTLIER) cc_final: 0.6252 (tmtt) outliers start: 47 outliers final: 27 residues processed: 271 average time/residue: 1.4672 time to fit residues: 430.5014 Evaluate side-chains 266 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 43 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 149 optimal weight: 0.0970 chunk 120 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 156 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 372 GLN C 372 GLN D 251 GLN E 139 ASN E 247 GLN E 251 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.118052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.091665 restraints weight = 16681.555| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.91 r_work: 0.2720 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14654 Z= 0.147 Angle : 0.591 20.629 19813 Z= 0.302 Chirality : 0.044 0.522 2239 Planarity : 0.004 0.045 2394 Dihedral : 7.813 59.763 2336 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.30 % Allowed : 11.32 % Favored : 85.38 % 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: 1.69 (0.21), residues: 1660 helix: 2.21 (0.23), residues: 560 sheet: 0.80 (0.24), residues: 440 loop : 0.52 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.005 0.001 HIS C 254 PHE 0.015 0.001 PHE B 92 TYR 0.015 0.002 TYR E 272 ARG 0.004 0.000 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00915 ( 10) link_NAG-ASN : angle 6.17012 ( 30) hydrogen bonds : bond 0.06855 ( 689) hydrogen bonds : angle 3.84222 ( 2130) covalent geometry : bond 0.00291 (14644) covalent geometry : angle 0.53997 (19783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 1.591 Fit side-chains revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8243 (ttp-170) cc_final: 0.7454 (ttm-80) REVERT: A 227 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.6702 (tmt) REVERT: A 269 ASN cc_start: 0.8540 (m110) cc_final: 0.8122 (m-40) REVERT: A 335 MET cc_start: 0.7748 (mtm) cc_final: 0.6724 (mmp) REVERT: A 345 ASP cc_start: 0.8244 (m-30) cc_final: 0.7866 (m-30) REVERT: B 151 LYS cc_start: 0.8516 (mmtt) cc_final: 0.7866 (mptt) REVERT: B 232 LYS cc_start: 0.8162 (mtmt) cc_final: 0.7922 (mtmt) REVERT: B 241 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6576 (mm-30) REVERT: B 278 ARG cc_start: 0.8160 (mtt-85) cc_final: 0.7783 (mtp85) REVERT: B 308 ARG cc_start: 0.7636 (mtm180) cc_final: 0.7309 (mtm110) REVERT: C 82 ASP cc_start: 0.7493 (m-30) cc_final: 0.6165 (p0) REVERT: C 88 MET cc_start: 0.8184 (ptp) cc_final: 0.7927 (ptt) REVERT: C 116 MET cc_start: 0.8618 (mtm) cc_final: 0.8065 (mtp) REVERT: C 151 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8080 (mmtp) REVERT: C 179 ARG cc_start: 0.8441 (ttp-170) cc_final: 0.7874 (ttm-80) REVERT: C 240 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6733 (t70) REVERT: C 242 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.5920 (mtt90) REVERT: D 114 VAL cc_start: 0.7634 (t) cc_final: 0.7288 (p) REVERT: D 179 ARG cc_start: 0.8034 (ttp-170) cc_final: 0.7596 (ttp-170) REVERT: E 106 GLU cc_start: 0.7995 (tt0) cc_final: 0.7408 (tt0) REVERT: E 111 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8078 (mt) REVERT: E 116 MET cc_start: 0.8722 (mtm) cc_final: 0.8457 (mtp) REVERT: E 232 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7417 (mmpt) REVERT: E 269 ASN cc_start: 0.8721 (m-40) cc_final: 0.8374 (m-40) REVERT: E 373 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6408 (tm-30) REVERT: E 375 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.6257 (tmtt) outliers start: 51 outliers final: 31 residues processed: 258 average time/residue: 1.4180 time to fit residues: 396.6394 Evaluate side-chains 261 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 38 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN C 251 GLN C 372 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN E 251 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.113323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.086494 restraints weight = 16826.750| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.88 r_work: 0.2674 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14654 Z= 0.200 Angle : 0.666 20.572 19813 Z= 0.347 Chirality : 0.046 0.482 2239 Planarity : 0.005 0.049 2394 Dihedral : 8.472 59.579 2336 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.01 % Allowed : 10.74 % Favored : 85.25 % 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: 1.66 (0.21), residues: 1660 helix: 2.37 (0.23), residues: 535 sheet: 0.83 (0.24), residues: 465 loop : 0.34 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 128 HIS 0.007 0.002 HIS C 254 PHE 0.018 0.002 PHE B 92 TYR 0.018 0.002 TYR B 123 ARG 0.003 0.000 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.01091 ( 10) link_NAG-ASN : angle 5.93760 ( 30) hydrogen bonds : bond 0.08179 ( 689) hydrogen bonds : angle 3.97033 ( 2130) covalent geometry : bond 0.00443 (14644) covalent geometry : angle 0.62564 (19783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 230 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8394 (ttp-170) cc_final: 0.7614 (ttm-80) REVERT: A 269 ASN cc_start: 0.8567 (m110) cc_final: 0.7727 (t0) REVERT: A 308 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7129 (mtp85) REVERT: A 335 MET cc_start: 0.7904 (mtm) cc_final: 0.6859 (mmp) REVERT: A 345 ASP cc_start: 0.8344 (m-30) cc_final: 0.7971 (m-30) REVERT: B 241 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6545 (mm-30) REVERT: B 308 ARG cc_start: 0.7726 (mtm180) cc_final: 0.7406 (mtm110) REVERT: B 337 ARG cc_start: 0.7811 (ttm-80) cc_final: 0.7583 (tpp-160) REVERT: C 82 ASP cc_start: 0.7550 (m-30) cc_final: 0.6276 (p0) REVERT: C 92 PHE cc_start: 0.8327 (t80) cc_final: 0.8017 (t80) REVERT: C 116 MET cc_start: 0.8766 (mtm) cc_final: 0.8235 (mtp) REVERT: C 151 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8275 (mmtp) REVERT: C 179 ARG cc_start: 0.8475 (ttp-170) cc_final: 0.7979 (ttm-80) REVERT: C 183 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7745 (p0) REVERT: C 238 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8197 (mptp) REVERT: C 242 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6247 (mtt90) REVERT: D 82 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.6124 (OUTLIER) REVERT: D 114 VAL cc_start: 0.7825 (t) cc_final: 0.7457 (p) REVERT: D 165 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8283 (ptt90) REVERT: D 179 ARG cc_start: 0.8194 (ttp-170) cc_final: 0.7784 (ttp-170) REVERT: D 247 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7753 (pt0) REVERT: D 457 LYS cc_start: 0.8198 (ttmp) cc_final: 0.7448 (ttpt) REVERT: E 106 GLU cc_start: 0.8010 (tt0) cc_final: 0.7425 (tt0) REVERT: E 111 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8154 (mt) REVERT: E 116 MET cc_start: 0.8861 (mtm) cc_final: 0.8555 (mtp) REVERT: E 232 LYS cc_start: 0.8313 (mtmm) cc_final: 0.7567 (mmpt) REVERT: E 269 ASN cc_start: 0.8802 (m-40) cc_final: 0.8397 (m-40) REVERT: E 373 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6551 (tm-30) REVERT: E 375 LYS cc_start: 0.6572 (OUTLIER) cc_final: 0.6365 (tmtt) outliers start: 62 outliers final: 34 residues processed: 268 average time/residue: 1.4591 time to fit residues: 423.3171 Evaluate side-chains 265 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 247 GLN C 287 GLN C 372 GLN D 251 GLN E 247 GLN E 251 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.091405 restraints weight = 16807.757| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.87 r_work: 0.2701 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14654 Z= 0.158 Angle : 0.605 20.086 19813 Z= 0.313 Chirality : 0.044 0.482 2239 Planarity : 0.004 0.048 2394 Dihedral : 8.300 59.613 2336 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.82 % Allowed : 11.51 % Favored : 84.67 % 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: 1.68 (0.21), residues: 1660 helix: 2.44 (0.23), residues: 535 sheet: 0.83 (0.24), residues: 465 loop : 0.31 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 128 HIS 0.005 0.001 HIS C 254 PHE 0.018 0.002 PHE B 92 TYR 0.015 0.002 TYR A 340 ARG 0.004 0.000 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.01073 ( 10) link_NAG-ASN : angle 5.93860 ( 30) hydrogen bonds : bond 0.07254 ( 689) hydrogen bonds : angle 3.86730 ( 2130) covalent geometry : bond 0.00321 (14644) covalent geometry : angle 0.55947 (19783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 224 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8300 (ttp-170) cc_final: 0.7458 (ttm-80) REVERT: A 227 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.6826 (tmt) REVERT: A 269 ASN cc_start: 0.8525 (m110) cc_final: 0.8140 (m-40) REVERT: A 308 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7101 (mtp85) REVERT: A 335 MET cc_start: 0.7813 (mtm) cc_final: 0.6809 (mmp) REVERT: A 345 ASP cc_start: 0.8308 (m-30) cc_final: 0.7931 (m-30) REVERT: B 241 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6467 (mm-30) REVERT: B 308 ARG cc_start: 0.7705 (mtm180) cc_final: 0.7394 (mtm110) REVERT: C 82 ASP cc_start: 0.7518 (m-30) cc_final: 0.6282 (p0) REVERT: C 111 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.7929 (mt) REVERT: C 116 MET cc_start: 0.8687 (mtm) cc_final: 0.8155 (mtp) REVERT: C 151 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8118 (mmtp) REVERT: C 179 ARG cc_start: 0.8428 (ttp-170) cc_final: 0.7934 (ttm-80) REVERT: C 181 GLN cc_start: 0.8512 (mm110) cc_final: 0.8199 (mt0) REVERT: C 183 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7686 (p0) REVERT: C 238 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8164 (mptp) REVERT: C 242 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6239 (mtt90) REVERT: D 114 VAL cc_start: 0.7765 (t) cc_final: 0.7419 (p) REVERT: D 179 ARG cc_start: 0.8131 (ttp-170) cc_final: 0.7728 (ttp-170) REVERT: D 247 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7737 (pt0) REVERT: D 457 LYS cc_start: 0.8153 (ttmp) cc_final: 0.7385 (ttpt) REVERT: E 106 GLU cc_start: 0.7962 (tt0) cc_final: 0.7424 (tt0) REVERT: E 111 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8143 (mt) REVERT: E 116 MET cc_start: 0.8792 (mtm) cc_final: 0.8473 (mtp) REVERT: E 232 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7528 (mmpt) REVERT: E 269 ASN cc_start: 0.8775 (m-40) cc_final: 0.8392 (m-40) REVERT: E 373 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6425 (tm-30) outliers start: 59 outliers final: 38 residues processed: 261 average time/residue: 1.4967 time to fit residues: 422.4434 Evaluate side-chains 264 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 61 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 247 GLN C 372 GLN D 251 GLN E 247 GLN E 251 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.111654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.084655 restraints weight = 17120.753| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 1.96 r_work: 0.2654 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14654 Z= 0.200 Angle : 0.659 20.016 19813 Z= 0.344 Chirality : 0.046 0.438 2239 Planarity : 0.005 0.051 2394 Dihedral : 8.745 58.924 2336 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.20 % Allowed : 11.84 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.54 (0.21), residues: 1660 helix: 2.33 (0.23), residues: 535 sheet: 0.77 (0.24), residues: 465 loop : 0.21 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 128 HIS 0.006 0.002 HIS C 254 PHE 0.020 0.002 PHE B 92 TYR 0.017 0.002 TYR B 123 ARG 0.002 0.000 ARG E 165 Details of bonding type rmsd link_NAG-ASN : bond 0.01082 ( 10) link_NAG-ASN : angle 5.64284 ( 30) hydrogen bonds : bond 0.08188 ( 689) hydrogen bonds : angle 3.96647 ( 2130) covalent geometry : bond 0.00446 (14644) covalent geometry : angle 0.62172 (19783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 228 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8402 (ttp-170) cc_final: 0.7502 (ttm-80) REVERT: A 181 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8072 (mm110) REVERT: A 227 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.6813 (tmt) REVERT: A 269 ASN cc_start: 0.8583 (m110) cc_final: 0.7686 (t0) REVERT: A 308 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7054 (mtp85) REVERT: A 335 MET cc_start: 0.7783 (mtm) cc_final: 0.6655 (mmp) REVERT: A 345 ASP cc_start: 0.8363 (m-30) cc_final: 0.7991 (m-30) REVERT: B 241 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6571 (mm-30) REVERT: B 308 ARG cc_start: 0.7603 (mtm180) cc_final: 0.7271 (mtm110) REVERT: C 82 ASP cc_start: 0.7577 (m-30) cc_final: 0.6326 (p0) REVERT: C 92 PHE cc_start: 0.8263 (t80) cc_final: 0.7977 (t80) REVERT: C 111 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.7934 (mt) REVERT: C 116 MET cc_start: 0.8648 (mtm) cc_final: 0.8103 (mtp) REVERT: C 151 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8197 (mmtp) REVERT: C 179 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.7875 (ttm-80) REVERT: C 183 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7756 (p0) REVERT: C 238 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8017 (mptp) REVERT: D 82 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.6074 (OUTLIER) REVERT: D 88 MET cc_start: 0.7777 (mtt) cc_final: 0.6882 (mmt) REVERT: D 114 VAL cc_start: 0.7678 (t) cc_final: 0.7300 (p) REVERT: D 165 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8236 (ptt90) REVERT: D 179 ARG cc_start: 0.8175 (ttp-170) cc_final: 0.7676 (ttp-170) REVERT: D 247 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7730 (pt0) REVERT: D 457 LYS cc_start: 0.8079 (ttmp) cc_final: 0.7280 (ttpt) REVERT: E 106 GLU cc_start: 0.7979 (tt0) cc_final: 0.7402 (tt0) REVERT: E 111 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8069 (mt) REVERT: E 116 MET cc_start: 0.8785 (mtm) cc_final: 0.8451 (mtp) REVERT: E 232 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7431 (mmpt) REVERT: E 269 ASN cc_start: 0.8868 (m-40) cc_final: 0.8377 (m-40) REVERT: E 373 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6303 (tm-30) REVERT: E 375 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.6232 (tmtt) outliers start: 65 outliers final: 42 residues processed: 273 average time/residue: 1.4521 time to fit residues: 429.4015 Evaluate side-chains 279 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 101 optimal weight: 0.0050 chunk 113 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 247 GLN C 251 GLN C 287 GLN C 372 GLN D 251 GLN E 247 GLN E 251 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.116141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.089104 restraints weight = 16885.833| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.97 r_work: 0.2715 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14654 Z= 0.132 Angle : 0.562 19.931 19813 Z= 0.289 Chirality : 0.043 0.442 2239 Planarity : 0.004 0.048 2394 Dihedral : 8.113 58.781 2336 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.17 % Allowed : 12.81 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.21), residues: 1660 helix: 2.58 (0.24), residues: 530 sheet: 0.86 (0.24), residues: 465 loop : 0.34 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 349 HIS 0.005 0.001 HIS C 254 PHE 0.018 0.001 PHE B 92 TYR 0.016 0.001 TYR A 340 ARG 0.002 0.000 ARG B 242 Details of bonding type rmsd link_NAG-ASN : bond 0.01098 ( 10) link_NAG-ASN : angle 5.75829 ( 30) hydrogen bonds : bond 0.06380 ( 689) hydrogen bonds : angle 3.75172 ( 2130) covalent geometry : bond 0.00245 (14644) covalent geometry : angle 0.51554 (19783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 1.817 Fit side-chains revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7359 (ttm-80) REVERT: A 181 GLN cc_start: 0.8264 (mm-40) cc_final: 0.8001 (mm110) REVERT: A 227 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.6746 (tmt) REVERT: A 308 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7034 (mtp85) REVERT: A 335 MET cc_start: 0.7635 (mtm) cc_final: 0.6567 (mmp) REVERT: A 345 ASP cc_start: 0.8237 (m-30) cc_final: 0.7875 (m-30) REVERT: A 457 LYS cc_start: 0.7800 (mttt) cc_final: 0.7361 (mtpm) REVERT: B 232 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7822 (mtmm) REVERT: B 241 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6410 (mm-30) REVERT: B 308 ARG cc_start: 0.7557 (mtm180) cc_final: 0.7233 (mtm110) REVERT: C 82 ASP cc_start: 0.7556 (m-30) cc_final: 0.6339 (p0) REVERT: C 92 PHE cc_start: 0.8258 (t80) cc_final: 0.7993 (t80) REVERT: C 111 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.7896 (mt) REVERT: C 116 MET cc_start: 0.8525 (mtm) cc_final: 0.8105 (mtp) REVERT: C 151 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8052 (mmtp) REVERT: C 179 ARG cc_start: 0.8351 (ttp-170) cc_final: 0.7797 (ttm-80) REVERT: C 183 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7609 (p0) REVERT: C 238 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8101 (mptp) REVERT: D 82 ASP cc_start: 0.6517 (OUTLIER) cc_final: 0.6082 (OUTLIER) REVERT: D 88 MET cc_start: 0.7849 (mtt) cc_final: 0.6870 (mmt) REVERT: D 114 VAL cc_start: 0.7573 (t) cc_final: 0.7217 (p) REVERT: D 179 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7545 (ttp-170) REVERT: D 247 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7732 (pt0) REVERT: D 457 LYS cc_start: 0.7930 (ttmp) cc_final: 0.7117 (ttpt) REVERT: E 106 GLU cc_start: 0.7946 (tt0) cc_final: 0.7427 (tt0) REVERT: E 111 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8038 (mt) REVERT: E 116 MET cc_start: 0.8636 (mtm) cc_final: 0.8307 (mtp) REVERT: E 232 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7364 (mmpt) REVERT: E 269 ASN cc_start: 0.8769 (m-40) cc_final: 0.8382 (m-40) REVERT: E 373 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6243 (tm-30) outliers start: 49 outliers final: 33 residues processed: 264 average time/residue: 1.5231 time to fit residues: 434.0627 Evaluate side-chains 268 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 135 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 73 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 247 GLN C 372 GLN D 251 GLN E 247 GLN E 251 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.111645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.084596 restraints weight = 16986.943| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 1.95 r_work: 0.2652 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14654 Z= 0.201 Angle : 0.672 20.974 19813 Z= 0.351 Chirality : 0.046 0.356 2239 Planarity : 0.005 0.050 2394 Dihedral : 8.587 59.107 2336 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.49 % Allowed : 12.94 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.21), residues: 1660 helix: 2.35 (0.23), residues: 535 sheet: 0.85 (0.24), residues: 460 loop : 0.10 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 230 HIS 0.006 0.002 HIS A 254 PHE 0.021 0.002 PHE B 92 TYR 0.017 0.002 TYR B 123 ARG 0.003 0.000 ARG B 278 Details of bonding type rmsd link_NAG-ASN : bond 0.01094 ( 10) link_NAG-ASN : angle 5.78407 ( 30) hydrogen bonds : bond 0.08160 ( 689) hydrogen bonds : angle 3.94190 ( 2130) covalent geometry : bond 0.00448 (14644) covalent geometry : angle 0.63316 (19783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8405 (ttp-170) cc_final: 0.7501 (ttm-80) REVERT: A 181 GLN cc_start: 0.8280 (mm-40) cc_final: 0.8067 (mm110) REVERT: A 227 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.6807 (tmt) REVERT: A 308 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7042 (mtp85) REVERT: A 335 MET cc_start: 0.7787 (mtm) cc_final: 0.6694 (mmp) REVERT: A 345 ASP cc_start: 0.8356 (m-30) cc_final: 0.7988 (m-30) REVERT: A 457 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7471 (mtpm) REVERT: B 241 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6519 (mm-30) REVERT: B 308 ARG cc_start: 0.7580 (mtm180) cc_final: 0.7244 (mtm110) REVERT: C 82 ASP cc_start: 0.7578 (m-30) cc_final: 0.6358 (p0) REVERT: C 92 PHE cc_start: 0.8265 (t80) cc_final: 0.8025 (t80) REVERT: C 111 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.7924 (mt) REVERT: C 116 MET cc_start: 0.8644 (mtm) cc_final: 0.8100 (mtp) REVERT: C 151 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8196 (mmtp) REVERT: C 179 ARG cc_start: 0.8435 (ttp-170) cc_final: 0.7876 (ttm-80) REVERT: C 183 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7731 (p0) REVERT: C 238 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8029 (mptp) REVERT: D 82 ASP cc_start: 0.6556 (OUTLIER) cc_final: 0.6072 (OUTLIER) REVERT: D 88 MET cc_start: 0.7872 (mtt) cc_final: 0.6913 (mmt) REVERT: D 114 VAL cc_start: 0.7668 (t) cc_final: 0.7283 (p) REVERT: D 165 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8242 (ptt90) REVERT: D 179 ARG cc_start: 0.8189 (ttp-170) cc_final: 0.7685 (ttp-170) REVERT: D 247 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7767 (pt0) REVERT: D 457 LYS cc_start: 0.8074 (ttmp) cc_final: 0.7271 (ttpt) REVERT: E 106 GLU cc_start: 0.8002 (tt0) cc_final: 0.7429 (tt0) REVERT: E 111 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8051 (mt) REVERT: E 116 MET cc_start: 0.8777 (mtm) cc_final: 0.8436 (mtp) REVERT: E 232 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7395 (mmpt) REVERT: E 269 ASN cc_start: 0.8870 (m-40) cc_final: 0.8380 (m-40) REVERT: E 373 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6305 (tm-30) outliers start: 54 outliers final: 39 residues processed: 266 average time/residue: 1.4684 time to fit residues: 422.9429 Evaluate side-chains 278 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 230 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 37 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 101 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 56 optimal weight: 0.0020 chunk 149 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 287 GLN B 247 GLN C 372 GLN D 251 GLN E 247 GLN E 251 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.094056 restraints weight = 16834.763| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.87 r_work: 0.2758 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14654 Z= 0.121 Angle : 0.532 20.395 19813 Z= 0.274 Chirality : 0.042 0.374 2239 Planarity : 0.004 0.048 2394 Dihedral : 7.713 57.111 2336 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.01 % Allowed : 14.49 % Favored : 83.51 % 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: 1.87 (0.21), residues: 1660 helix: 2.64 (0.24), residues: 530 sheet: 0.93 (0.24), residues: 470 loop : 0.39 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 349 HIS 0.003 0.001 HIS C 254 PHE 0.021 0.001 PHE B 92 TYR 0.016 0.001 TYR A 340 ARG 0.002 0.000 ARG C 191 Details of bonding type rmsd link_NAG-ASN : bond 0.01084 ( 10) link_NAG-ASN : angle 5.48668 ( 30) hydrogen bonds : bond 0.05734 ( 689) hydrogen bonds : angle 3.68440 ( 2130) covalent geometry : bond 0.00221 (14644) covalent geometry : angle 0.48728 (19783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.7360 (ttm-80) REVERT: A 181 GLN cc_start: 0.8302 (mm-40) cc_final: 0.8092 (mm110) REVERT: A 227 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.6791 (tmt) REVERT: A 308 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6992 (mtp85) REVERT: A 335 MET cc_start: 0.7653 (mtm) cc_final: 0.6576 (mmp) REVERT: A 345 ASP cc_start: 0.8175 (m-30) cc_final: 0.7819 (m-30) REVERT: A 457 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7448 (mtpm) REVERT: B 108 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8204 (mp) REVERT: B 232 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7908 (mtmm) REVERT: B 241 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6457 (mm-30) REVERT: B 308 ARG cc_start: 0.7616 (mtm180) cc_final: 0.7315 (mtm110) REVERT: C 82 ASP cc_start: 0.7539 (m-30) cc_final: 0.6378 (p0) REVERT: C 111 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.7900 (mt) REVERT: C 116 MET cc_start: 0.8556 (mtm) cc_final: 0.8141 (mtp) REVERT: C 151 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8146 (mmtp) REVERT: C 179 ARG cc_start: 0.8327 (ttp-170) cc_final: 0.7819 (ttm-80) REVERT: C 183 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7664 (p0) REVERT: D 88 MET cc_start: 0.7857 (mtt) cc_final: 0.6908 (mmt) REVERT: D 114 VAL cc_start: 0.7628 (t) cc_final: 0.7284 (p) REVERT: D 179 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7583 (ttp-170) REVERT: D 457 LYS cc_start: 0.8000 (ttmp) cc_final: 0.7225 (ttpt) REVERT: E 106 GLU cc_start: 0.7918 (tt0) cc_final: 0.7431 (tt0) REVERT: E 111 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8075 (mt) REVERT: E 116 MET cc_start: 0.8649 (mtm) cc_final: 0.8337 (mtp) REVERT: E 232 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7455 (mmpt) REVERT: E 263 SER cc_start: 0.8170 (p) cc_final: 0.7933 (t) REVERT: E 269 ASN cc_start: 0.8705 (m-40) cc_final: 0.8406 (m-40) REVERT: E 373 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6258 (tm-30) outliers start: 31 outliers final: 19 residues processed: 261 average time/residue: 1.5435 time to fit residues: 434.6411 Evaluate side-chains 254 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 125 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 247 GLN C 251 GLN C 372 GLN E 247 GLN E 251 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.117977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.091151 restraints weight = 16889.324| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.94 r_work: 0.2737 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14654 Z= 0.126 Angle : 0.546 20.239 19813 Z= 0.282 Chirality : 0.042 0.388 2239 Planarity : 0.004 0.048 2394 Dihedral : 7.501 58.753 2336 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.01 % Allowed : 14.68 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.21), residues: 1660 helix: 2.72 (0.24), residues: 530 sheet: 0.96 (0.24), residues: 470 loop : 0.42 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 349 HIS 0.004 0.001 HIS C 254 PHE 0.020 0.001 PHE B 92 TYR 0.016 0.001 TYR A 340 ARG 0.002 0.000 ARG D 337 Details of bonding type rmsd link_NAG-ASN : bond 0.01097 ( 10) link_NAG-ASN : angle 5.37468 ( 30) hydrogen bonds : bond 0.05889 ( 689) hydrogen bonds : angle 3.61719 ( 2130) covalent geometry : bond 0.00235 (14644) covalent geometry : angle 0.50476 (19783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10468.03 seconds wall clock time: 180 minutes 55.37 seconds (10855.37 seconds total)