Starting phenix.real_space_refine on Fri Jun 13 04:39:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oq8_17108/06_2025/8oq8_17108.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oq8_17108/06_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_17108/06_2025/8oq8_17108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oq8_17108/06_2025/8oq8_17108.map" model { file = "/net/cci-nas-00/data/ceres_data/8oq8_17108/06_2025/8oq8_17108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oq8_17108/06_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-5710/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: 10.73, per 1000 atoms: 0.74 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: 3.75 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: 1.86 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: 4.38 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: 6.350 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.520 Find NCS groups from input model: 0.830 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 57.140 ------------------------------------------------------------------------------- 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 : 1.718 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: 1.6434 time to fit residues: 532.6390 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 : 1.561 ------------------------------------------------------------------------------- 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 = 0.120982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.094912 restraints weight = 16560.741| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.90 r_work: 0.2744 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 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 23.444 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 4.23897 ( 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 : 1.725 Fit side-chains REVERT: A 179 ARG cc_start: 0.8188 (ttp-170) cc_final: 0.7409 (ttm-80) REVERT: A 269 ASN cc_start: 0.8546 (m110) cc_final: 0.8206 (m-40) REVERT: A 335 MET cc_start: 0.7787 (mtm) cc_final: 0.6757 (mmp) REVERT: A 345 ASP cc_start: 0.8283 (m-30) cc_final: 0.7887 (m-30) REVERT: B 151 LYS cc_start: 0.8492 (mmtt) cc_final: 0.7859 (mptt) REVERT: B 241 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6628 (mm-30) REVERT: B 269 ASN cc_start: 0.8414 (m-40) cc_final: 0.8199 (m-40) REVERT: B 278 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7954 (mtp85) REVERT: B 308 ARG cc_start: 0.7633 (mtm180) cc_final: 0.7311 (mtm110) REVERT: C 82 ASP cc_start: 0.7451 (m-30) cc_final: 0.6080 (p0) REVERT: C 116 MET cc_start: 0.8596 (mtm) cc_final: 0.8040 (mtp) REVERT: C 151 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8093 (mmtp) REVERT: C 179 ARG cc_start: 0.8419 (ttp-170) cc_final: 0.7873 (ttm-80) REVERT: C 235 ASP cc_start: 0.8222 (m-30) cc_final: 0.7969 (m-30) REVERT: C 242 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.6208 (mtt90) REVERT: D 113 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7859 (mt-10) REVERT: D 114 VAL cc_start: 0.7624 (t) cc_final: 0.7325 (p) REVERT: D 179 ARG cc_start: 0.8130 (ttp-170) cc_final: 0.7655 (ttp-170) REVERT: E 106 GLU cc_start: 0.7986 (tt0) cc_final: 0.7425 (tt0) REVERT: E 116 MET cc_start: 0.8659 (mtm) cc_final: 0.8410 (mtp) REVERT: E 232 LYS cc_start: 0.8359 (mtmm) cc_final: 0.7509 (mmpt) REVERT: E 269 ASN cc_start: 0.8700 (m-40) cc_final: 0.8267 (t0) REVERT: E 373 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6551 (tm-30) REVERT: E 375 LYS cc_start: 0.6384 (tmtt) cc_final: 0.6137 (tmtt) outliers start: 33 outliers final: 14 residues processed: 277 average time/residue: 1.4315 time to fit residues: 429.4425 Evaluate side-chains 260 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 245 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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: 0.9980 chunk 149 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 138 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN A 372 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 = 0.3199 r_free = 0.3199 target = 0.115143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.088067 restraints weight = 16754.636| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.95 r_work: 0.2690 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14654 Z= 0.167 Angle : 0.639 22.134 19813 Z= 0.327 Chirality : 0.045 0.561 2239 Planarity : 0.004 0.043 2394 Dihedral : 8.282 59.953 2338 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.36 % Allowed : 10.28 % Favored : 86.35 % 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: 1.59 (0.20), residues: 1660 helix: 2.07 (0.23), residues: 565 sheet: 0.76 (0.24), residues: 440 loop : 0.50 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.006 0.001 HIS C 254 PHE 0.015 0.002 PHE B 92 TYR 0.016 0.002 TYR E 272 ARG 0.004 0.000 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00772 ( 10) link_NAG-ASN : angle 6.76295 ( 30) hydrogen bonds : bond 0.07696 ( 689) hydrogen bonds : angle 4.08232 ( 2130) covalent geometry : bond 0.00346 (14644) covalent geometry : angle 0.58244 (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 286 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8314 (ttp-170) cc_final: 0.7435 (ttm-80) REVERT: A 269 ASN cc_start: 0.8555 (m110) cc_final: 0.8115 (m-40) REVERT: A 335 MET cc_start: 0.7782 (mtm) cc_final: 0.6721 (mmp) REVERT: A 337 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6835 (mtm-85) REVERT: A 345 ASP cc_start: 0.8296 (m-30) cc_final: 0.7907 (m-30) REVERT: A 372 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7314 (tp-100) REVERT: B 151 LYS cc_start: 0.8539 (mmtt) cc_final: 0.7892 (mptt) REVERT: B 158 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8751 (mpm) REVERT: B 232 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7935 (mtmt) REVERT: B 241 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6617 (mm-30) REVERT: B 269 ASN cc_start: 0.8526 (m-40) cc_final: 0.8189 (m-40) REVERT: B 278 ARG cc_start: 0.8176 (mtt-85) cc_final: 0.7785 (mtp85) REVERT: B 308 ARG cc_start: 0.7650 (mtm180) cc_final: 0.7333 (mtm110) REVERT: B 337 ARG cc_start: 0.7752 (ttm-80) cc_final: 0.7526 (tpp-160) REVERT: C 82 ASP cc_start: 0.7550 (m-30) cc_final: 0.6221 (p0) REVERT: C 88 MET cc_start: 0.8210 (ptp) cc_final: 0.8000 (ptt) REVERT: C 116 MET cc_start: 0.8648 (mtm) cc_final: 0.8087 (mtp) REVERT: C 151 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8059 (mmtp) REVERT: C 179 ARG cc_start: 0.8470 (ttp-170) cc_final: 0.7909 (ttm-80) REVERT: C 223 GLU cc_start: 0.7693 (pt0) cc_final: 0.7470 (tp30) REVERT: C 242 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6207 (mtt90) REVERT: D 114 VAL cc_start: 0.7660 (t) cc_final: 0.7318 (p) REVERT: D 179 ARG cc_start: 0.8144 (ttp-170) cc_final: 0.7686 (ttp-170) REVERT: D 457 LYS cc_start: 0.8064 (ttmp) cc_final: 0.7269 (ttpt) REVERT: E 106 GLU cc_start: 0.8001 (tt0) cc_final: 0.7416 (tt0) REVERT: E 111 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8077 (mt) REVERT: E 116 MET cc_start: 0.8754 (mtm) cc_final: 0.8493 (mtp) REVERT: E 232 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7473 (mmpt) REVERT: E 269 ASN cc_start: 0.8777 (m-40) cc_final: 0.8393 (m-40) REVERT: E 373 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6556 (tm-30) REVERT: E 375 LYS cc_start: 0.6447 (OUTLIER) cc_final: 0.6224 (tmtt) outliers start: 52 outliers final: 28 residues processed: 265 average time/residue: 1.4499 time to fit residues: 416.2578 Evaluate side-chains 262 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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 337 ARG Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 158 MET 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 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 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 E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 43 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 199 ASN A 287 GLN A 372 GLN C 287 GLN C 372 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN 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 = 0.3231 r_free = 0.3231 target = 0.117131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.090981 restraints weight = 16667.669| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.87 r_work: 0.2698 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1672 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= 0.166 Angle : 0.623 20.731 19813 Z= 0.321 Chirality : 0.045 0.510 2239 Planarity : 0.004 0.046 2394 Dihedral : 8.306 59.522 2336 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.69 % Allowed : 10.74 % Favored : 85.58 % 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: 1.48 (0.20), residues: 1660 helix: 2.03 (0.23), residues: 565 sheet: 0.70 (0.24), residues: 440 loop : 0.37 (0.22), residues: 655 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 0.016 0.002 PHE B 92 TYR 0.016 0.002 TYR E 272 ARG 0.003 0.000 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00935 ( 10) link_NAG-ASN : angle 6.18702 ( 30) hydrogen bonds : bond 0.07485 ( 689) hydrogen bonds : angle 3.95014 ( 2130) covalent geometry : bond 0.00344 (14644) covalent geometry : angle 0.57489 (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 282 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8306 (ttp-170) cc_final: 0.7461 (ttm-80) REVERT: A 227 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.6875 (tmt) REVERT: A 269 ASN cc_start: 0.8537 (m110) cc_final: 0.8101 (m-40) REVERT: A 335 MET cc_start: 0.7799 (mtm) cc_final: 0.6750 (mmp) REVERT: A 337 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6836 (mtm-85) REVERT: A 345 ASP cc_start: 0.8280 (m-30) cc_final: 0.7894 (m-30) REVERT: B 158 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8767 (mpm) REVERT: B 232 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7965 (mtmt) REVERT: B 241 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6552 (mm-30) REVERT: B 269 ASN cc_start: 0.8537 (m-40) cc_final: 0.8204 (m-40) REVERT: B 308 ARG cc_start: 0.7675 (mtm180) cc_final: 0.7366 (mtm110) REVERT: C 82 ASP cc_start: 0.7589 (m-30) cc_final: 0.6281 (p0) REVERT: C 88 MET cc_start: 0.8256 (ptp) cc_final: 0.8007 (ptt) REVERT: C 111 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.7968 (mt) REVERT: C 116 MET cc_start: 0.8671 (mtm) cc_final: 0.8117 (mtp) REVERT: C 151 LYS cc_start: 0.8488 (mmtt) cc_final: 0.8083 (mmtp) REVERT: C 179 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.7933 (ttm-80) REVERT: C 183 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7694 (p0) REVERT: C 242 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6239 (mtt90) REVERT: D 82 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.6111 (OUTLIER) REVERT: D 114 VAL cc_start: 0.7744 (t) cc_final: 0.7391 (p) REVERT: D 179 ARG cc_start: 0.8105 (ttp-170) cc_final: 0.7685 (ttp-170) REVERT: D 457 LYS cc_start: 0.8128 (ttmp) cc_final: 0.7350 (ttpt) REVERT: E 106 GLU cc_start: 0.7966 (tt0) cc_final: 0.7396 (tt0) REVERT: E 111 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8098 (mt) REVERT: E 116 MET cc_start: 0.8767 (mtm) cc_final: 0.8454 (mtp) REVERT: E 232 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7472 (mmpt) REVERT: E 269 ASN cc_start: 0.8767 (m-40) cc_final: 0.8394 (m-40) REVERT: E 373 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6476 (tm-30) REVERT: E 375 LYS cc_start: 0.6485 (OUTLIER) cc_final: 0.6272 (tmtt) outliers start: 57 outliers final: 34 residues processed: 263 average time/residue: 1.5246 time to fit residues: 433.5117 Evaluate side-chains 264 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 1.571 ------------------------------------------------------------------------------- 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 A residue 337 ARG Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 158 MET 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 111 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 239 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 38 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 158 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 125 optimal weight: 0.2980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 B 247 GLN C 251 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 = 0.3182 r_free = 0.3182 target = 0.113958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.087195 restraints weight = 16837.113| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.88 r_work: 0.2686 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14654 Z= 0.175 Angle : 0.629 20.512 19813 Z= 0.327 Chirality : 0.045 0.473 2239 Planarity : 0.005 0.049 2394 Dihedral : 8.530 59.670 2336 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.40 % Allowed : 10.67 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.39 (0.23), residues: 535 sheet: 0.81 (0.24), residues: 465 loop : 0.33 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.006 0.002 HIS C 254 PHE 0.017 0.002 PHE B 92 TYR 0.016 0.002 TYR B 123 ARG 0.002 0.000 ARG B 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00962 ( 10) link_NAG-ASN : angle 5.82342 ( 30) hydrogen bonds : bond 0.07693 ( 689) hydrogen bonds : angle 3.93056 ( 2130) covalent geometry : bond 0.00371 (14644) covalent geometry : angle 0.58760 (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 296 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8347 (ttp-170) cc_final: 0.7560 (ttm-80) REVERT: A 227 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.6896 (tmt) REVERT: A 269 ASN cc_start: 0.8541 (m110) cc_final: 0.7713 (t0) REVERT: A 308 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7127 (mtp85) REVERT: A 335 MET cc_start: 0.7848 (mtm) cc_final: 0.6832 (mmp) REVERT: A 337 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6857 (mtm-85) REVERT: A 345 ASP cc_start: 0.8309 (m-30) cc_final: 0.7899 (m-30) REVERT: A 372 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7333 (tp-100) REVERT: B 158 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8788 (mpm) REVERT: B 232 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7985 (mtmt) REVERT: B 241 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6559 (mm-30) REVERT: B 269 ASN cc_start: 0.8573 (m-40) cc_final: 0.8233 (m-40) REVERT: B 308 ARG cc_start: 0.7707 (mtm180) cc_final: 0.7399 (mtm110) REVERT: C 82 ASP cc_start: 0.7543 (m-30) cc_final: 0.6318 (p0) REVERT: C 88 MET cc_start: 0.8282 (ptp) cc_final: 0.8039 (ptt) REVERT: C 92 PHE cc_start: 0.8319 (t80) cc_final: 0.8060 (t80) REVERT: C 116 MET cc_start: 0.8720 (mtm) cc_final: 0.8191 (mtp) REVERT: C 151 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8113 (mmtp) REVERT: C 179 ARG cc_start: 0.8465 (ttp-170) cc_final: 0.7946 (ttm-80) REVERT: C 181 GLN cc_start: 0.8536 (mm110) cc_final: 0.8235 (mt0) REVERT: C 183 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7716 (p0) REVERT: C 242 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6251 (mtt90) REVERT: D 82 ASP cc_start: 0.6541 (OUTLIER) cc_final: 0.6130 (OUTLIER) REVERT: D 114 VAL cc_start: 0.7797 (t) cc_final: 0.7431 (p) REVERT: D 165 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8268 (ptt90) REVERT: D 179 ARG cc_start: 0.8151 (ttp-170) cc_final: 0.7735 (ttp-170) REVERT: D 247 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: D 457 LYS cc_start: 0.8174 (ttmp) cc_final: 0.7413 (ttpt) REVERT: E 106 GLU cc_start: 0.7963 (tt0) cc_final: 0.7430 (tt0) REVERT: E 111 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8122 (mt) REVERT: E 116 MET cc_start: 0.8821 (mtm) cc_final: 0.8508 (mtp) REVERT: E 232 LYS cc_start: 0.8284 (mtmm) cc_final: 0.7556 (mmpt) REVERT: E 269 ASN cc_start: 0.8778 (m-40) cc_final: 0.8389 (m-40) REVERT: E 373 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6447 (tm-30) REVERT: E 375 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.6339 (tmtt) outliers start: 68 outliers final: 42 residues processed: 271 average time/residue: 1.6543 time to fit residues: 487.1245 Evaluate side-chains 279 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 337 ARG Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 158 MET 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 131 GLU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 194 VAL 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 178 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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 = 0.118049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.091858 restraints weight = 16853.273| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.88 r_work: 0.2732 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14654 Z= 0.132 Angle : 0.563 20.380 19813 Z= 0.289 Chirality : 0.043 0.417 2239 Planarity : 0.004 0.047 2394 Dihedral : 8.098 59.656 2336 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.98 % Allowed : 12.42 % Favored : 84.61 % 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: 1.81 (0.21), residues: 1660 helix: 2.60 (0.24), residues: 530 sheet: 0.88 (0.24), residues: 465 loop : 0.37 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 128 HIS 0.004 0.001 HIS C 254 PHE 0.018 0.001 PHE B 92 TYR 0.016 0.002 TYR A 340 ARG 0.002 0.000 ARG A 374 Details of bonding type rmsd link_NAG-ASN : bond 0.01144 ( 10) link_NAG-ASN : angle 5.90329 ( 30) hydrogen bonds : bond 0.06457 ( 689) hydrogen bonds : angle 3.77382 ( 2130) covalent geometry : bond 0.00243 (14644) covalent geometry : angle 0.51468 (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 277 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8240 (ttp-170) cc_final: 0.7422 (ttm-80) REVERT: A 227 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.6826 (tmt) REVERT: A 308 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7077 (mtp85) REVERT: A 335 MET cc_start: 0.7699 (mtm) cc_final: 0.6680 (mmp) REVERT: A 345 ASP cc_start: 0.8236 (m-30) cc_final: 0.7859 (m-30) REVERT: A 457 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7512 (mtpm) REVERT: B 232 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7828 (mtmm) REVERT: B 241 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6420 (mm-30) REVERT: B 269 ASN cc_start: 0.8472 (m-40) cc_final: 0.8178 (m-40) REVERT: B 308 ARG cc_start: 0.7645 (mtm180) cc_final: 0.7336 (mtm110) REVERT: C 82 ASP cc_start: 0.7514 (m-30) cc_final: 0.6307 (p0) REVERT: C 111 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.7850 (mt) REVERT: C 116 MET cc_start: 0.8613 (mtm) cc_final: 0.8074 (mtp) REVERT: C 151 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8103 (mmtp) REVERT: C 179 ARG cc_start: 0.8399 (ttp-170) cc_final: 0.7863 (ttm-80) REVERT: C 181 GLN cc_start: 0.8473 (mm110) cc_final: 0.8181 (mt0) REVERT: C 242 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6218 (mtt90) REVERT: D 114 VAL cc_start: 0.7646 (t) cc_final: 0.7294 (p) REVERT: D 165 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8206 (ptt90) REVERT: D 179 ARG cc_start: 0.8023 (ttp-170) cc_final: 0.7605 (ttp-170) REVERT: D 247 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7740 (pt0) REVERT: D 457 LYS cc_start: 0.8050 (ttmp) cc_final: 0.7282 (ttpt) REVERT: E 106 GLU cc_start: 0.7932 (tt0) cc_final: 0.7391 (tt0) REVERT: E 116 MET cc_start: 0.8716 (mtm) cc_final: 0.8411 (mtp) REVERT: E 232 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7455 (mmpt) REVERT: E 269 ASN cc_start: 0.8723 (m-40) cc_final: 0.8386 (m-40) REVERT: E 373 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6363 (tm-30) outliers start: 46 outliers final: 30 residues processed: 261 average time/residue: 1.5479 time to fit residues: 435.6407 Evaluate side-chains 263 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 242 ARG Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 212 CYS 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 D residue 462 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 241 GLU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 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: 4.9990 chunk 144 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 ** 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 = 0.3159 r_free = 0.3159 target = 0.111924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.084995 restraints weight = 17122.071| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.95 r_work: 0.2661 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14654 Z= 0.189 Angle : 0.642 20.223 19813 Z= 0.335 Chirality : 0.045 0.442 2239 Planarity : 0.005 0.049 2394 Dihedral : 8.684 59.898 2336 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.69 % Allowed : 12.23 % Favored : 84.09 % 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: 1.60 (0.21), residues: 1660 helix: 2.38 (0.23), residues: 535 sheet: 0.77 (0.24), residues: 465 loop : 0.27 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.006 0.002 HIS A 254 PHE 0.019 0.002 PHE B 92 TYR 0.016 0.002 TYR B 123 ARG 0.002 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01095 ( 10) link_NAG-ASN : angle 5.54758 ( 30) hydrogen bonds : bond 0.07991 ( 689) hydrogen bonds : angle 3.93582 ( 2130) covalent geometry : bond 0.00413 (14644) covalent geometry : angle 0.60461 (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 288 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 231 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8374 (ttp-170) cc_final: 0.7495 (ttm-80) REVERT: A 181 GLN cc_start: 0.8273 (mm-40) cc_final: 0.8053 (mm110) REVERT: A 227 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.6835 (tmt) REVERT: A 308 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7009 (mtp85) REVERT: A 335 MET cc_start: 0.7783 (mtm) cc_final: 0.6648 (mmp) REVERT: A 345 ASP cc_start: 0.8341 (m-30) cc_final: 0.7953 (m-30) REVERT: A 457 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7480 (mtpm) REVERT: B 232 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7797 (mtmm) REVERT: B 241 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6501 (mm-30) REVERT: B 269 ASN cc_start: 0.8594 (m-40) cc_final: 0.8206 (m-40) REVERT: B 308 ARG cc_start: 0.7596 (mtm180) cc_final: 0.7272 (mtm110) REVERT: C 82 ASP cc_start: 0.7578 (m-30) cc_final: 0.6347 (p0) REVERT: C 92 PHE cc_start: 0.8277 (t80) cc_final: 0.7996 (t80) REVERT: C 111 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.7922 (mt) REVERT: C 116 MET cc_start: 0.8634 (mtm) cc_final: 0.8093 (mtp) REVERT: C 151 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8214 (mmtp) REVERT: C 179 ARG cc_start: 0.8439 (ttp-170) cc_final: 0.7885 (ttm-80) REVERT: C 181 GLN cc_start: 0.8470 (mm110) cc_final: 0.8184 (mt0) REVERT: C 183 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7715 (p0) REVERT: C 242 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6192 (mtt90) REVERT: D 82 ASP cc_start: 0.6537 (OUTLIER) cc_final: 0.6075 (OUTLIER) REVERT: D 88 MET cc_start: 0.7764 (mtt) cc_final: 0.6886 (mmt) REVERT: D 114 VAL cc_start: 0.7662 (t) cc_final: 0.7283 (p) REVERT: D 165 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8262 (ptt90) REVERT: D 179 ARG cc_start: 0.8176 (ttp-170) cc_final: 0.7679 (ttp-170) REVERT: D 247 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7729 (pt0) REVERT: D 457 LYS cc_start: 0.8074 (ttmp) cc_final: 0.7299 (ttpt) REVERT: E 106 GLU cc_start: 0.7956 (tt0) cc_final: 0.7385 (tt0) REVERT: E 111 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8085 (mt) REVERT: E 116 MET cc_start: 0.8775 (mtm) cc_final: 0.8449 (mtp) REVERT: E 232 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7404 (mmpt) REVERT: E 269 ASN cc_start: 0.8855 (m-40) cc_final: 0.8380 (m-40) REVERT: E 373 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6287 (tm-30) outliers start: 57 outliers final: 36 residues processed: 269 average time/residue: 1.4687 time to fit residues: 428.6575 Evaluate side-chains 273 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 301 VAL Chi-restraints excluded: chain A residue 307 ARG 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 122 LEU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 242 ARG 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 101 optimal weight: 0.0060 chunk 113 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3182 r_free = 0.3182 target = 0.113701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.086847 restraints weight = 16924.534| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.95 r_work: 0.2691 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14654 Z= 0.150 Angle : 0.582 20.464 19813 Z= 0.303 Chirality : 0.043 0.393 2239 Planarity : 0.004 0.047 2394 Dihedral : 8.329 59.300 2336 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.69 % Allowed : 12.10 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.21), residues: 1660 helix: 2.47 (0.23), residues: 535 sheet: 0.79 (0.24), residues: 465 loop : 0.29 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 128 HIS 0.005 0.001 HIS C 254 PHE 0.019 0.001 PHE B 92 TYR 0.015 0.002 TYR A 340 ARG 0.002 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01090 ( 10) link_NAG-ASN : angle 5.45021 ( 30) hydrogen bonds : bond 0.07002 ( 689) hydrogen bonds : angle 3.82163 ( 2130) covalent geometry : bond 0.00301 (14644) covalent geometry : angle 0.54194 (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 287 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8310 (ttp-170) cc_final: 0.7354 (ttm-80) REVERT: A 181 GLN cc_start: 0.8260 (mm-40) cc_final: 0.8016 (mm110) REVERT: A 227 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.6845 (tmt) REVERT: A 308 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7034 (mtp85) REVERT: A 335 MET cc_start: 0.7706 (mtm) cc_final: 0.6635 (mmp) REVERT: A 345 ASP cc_start: 0.8281 (m-30) cc_final: 0.7908 (m-30) REVERT: A 457 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7420 (mtpm) REVERT: B 232 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7780 (mtmm) REVERT: B 241 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6462 (mm-30) REVERT: B 269 ASN cc_start: 0.8542 (m-40) cc_final: 0.8202 (m-40) REVERT: B 308 ARG cc_start: 0.7577 (mtm180) cc_final: 0.7261 (mtm110) REVERT: C 82 ASP cc_start: 0.7552 (m-30) cc_final: 0.6348 (p0) REVERT: C 92 PHE cc_start: 0.8270 (t80) cc_final: 0.7990 (t80) REVERT: C 111 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.7921 (mt) REVERT: C 116 MET cc_start: 0.8576 (mtm) cc_final: 0.8037 (mtp) REVERT: C 151 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8011 (mmtp) REVERT: C 179 ARG cc_start: 0.8406 (ttp-170) cc_final: 0.7826 (ttm-80) REVERT: C 181 GLN cc_start: 0.8453 (mm110) cc_final: 0.8162 (mt0) REVERT: C 183 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7655 (p0) REVERT: C 242 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6156 (mtt90) REVERT: D 88 MET cc_start: 0.7830 (mtt) cc_final: 0.6900 (mmt) REVERT: D 114 VAL cc_start: 0.7621 (t) cc_final: 0.7256 (p) REVERT: D 165 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8218 (ptt90) REVERT: D 179 ARG cc_start: 0.8069 (ttp-170) cc_final: 0.7591 (ttp-170) REVERT: D 247 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: D 337 ARG cc_start: 0.8009 (mmt180) cc_final: 0.7797 (mmt90) REVERT: D 457 LYS cc_start: 0.8004 (ttmp) cc_final: 0.7204 (ttpt) REVERT: E 106 GLU cc_start: 0.7954 (tt0) cc_final: 0.7431 (tt0) REVERT: E 111 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8071 (mt) REVERT: E 116 MET cc_start: 0.8702 (mtm) cc_final: 0.8372 (mtp) REVERT: E 232 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7378 (mmpt) REVERT: E 269 ASN cc_start: 0.8815 (m-40) cc_final: 0.8390 (m-40) REVERT: E 373 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6251 (tm-30) outliers start: 57 outliers final: 42 residues processed: 270 average time/residue: 1.5437 time to fit residues: 449.8217 Evaluate side-chains 276 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 1.682 ------------------------------------------------------------------------------- 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 212 CYS 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 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 242 ARG Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 111 ILE 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 D residue 462 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 476 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 135 optimal weight: 0.0170 chunk 39 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 139 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 overall best weight: 0.8420 ------------------------------------------------------------------------------- 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 ** 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 = 0.3207 r_free = 0.3207 target = 0.115513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.088603 restraints weight = 16985.934| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.95 r_work: 0.2714 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14654 Z= 0.134 Angle : 0.553 20.090 19813 Z= 0.287 Chirality : 0.042 0.409 2239 Planarity : 0.004 0.046 2394 Dihedral : 7.950 57.924 2336 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.17 % Allowed : 12.87 % 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: 1.78 (0.21), residues: 1660 helix: 2.62 (0.24), residues: 530 sheet: 0.83 (0.24), residues: 465 loop : 0.34 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 349 HIS 0.004 0.001 HIS A 254 PHE 0.019 0.001 PHE B 92 TYR 0.016 0.002 TYR A 340 ARG 0.002 0.000 ARG D 313 Details of bonding type rmsd link_NAG-ASN : bond 0.01085 ( 10) link_NAG-ASN : angle 5.30196 ( 30) hydrogen bonds : bond 0.06419 ( 689) hydrogen bonds : angle 3.72915 ( 2130) covalent geometry : bond 0.00258 (14644) covalent geometry : angle 0.51317 (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 271 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 222 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8244 (ttp-170) cc_final: 0.7368 (ttm-80) REVERT: A 227 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.6825 (tmt) REVERT: A 308 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6993 (mtp85) REVERT: A 335 MET cc_start: 0.7682 (mtm) cc_final: 0.6575 (mmp) REVERT: A 345 ASP cc_start: 0.8242 (m-30) cc_final: 0.7876 (m-30) REVERT: A 457 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7389 (mtpm) REVERT: B 232 LYS cc_start: 0.8100 (mtmt) cc_final: 0.7789 (mtmm) REVERT: B 241 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6434 (mm-30) REVERT: B 269 ASN cc_start: 0.8461 (m-40) cc_final: 0.8165 (m-40) REVERT: B 308 ARG cc_start: 0.7565 (mtm180) cc_final: 0.7253 (mtm110) REVERT: C 82 ASP cc_start: 0.7582 (m-30) cc_final: 0.6386 (p0) REVERT: C 92 PHE cc_start: 0.8276 (t80) cc_final: 0.8002 (t80) REVERT: C 111 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.7895 (mt) REVERT: C 116 MET cc_start: 0.8569 (mtm) cc_final: 0.8157 (mtp) REVERT: C 151 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8066 (mmtp) REVERT: C 179 ARG cc_start: 0.8369 (ttp-170) cc_final: 0.7814 (ttm-80) REVERT: C 181 GLN cc_start: 0.8449 (mm110) cc_final: 0.8150 (mt0) REVERT: C 183 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7664 (p0) REVERT: C 242 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.6183 (mtt90) REVERT: D 82 ASP cc_start: 0.6491 (OUTLIER) cc_final: 0.6030 (OUTLIER) REVERT: D 88 MET cc_start: 0.7827 (mtt) cc_final: 0.6879 (mmt) REVERT: D 114 VAL cc_start: 0.7610 (t) cc_final: 0.7251 (p) REVERT: D 165 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8202 (ptt90) REVERT: D 247 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: D 337 ARG cc_start: 0.8014 (mmt180) cc_final: 0.7806 (mmt90) REVERT: D 457 LYS cc_start: 0.7986 (ttmp) cc_final: 0.7185 (ttpt) REVERT: E 106 GLU cc_start: 0.7938 (tt0) cc_final: 0.7426 (tt0) REVERT: E 111 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8061 (mt) REVERT: E 116 MET cc_start: 0.8687 (mtm) cc_final: 0.8366 (mtp) REVERT: E 232 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7382 (mmpt) REVERT: E 269 ASN cc_start: 0.8773 (m-40) cc_final: 0.8398 (m-40) REVERT: E 373 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6243 (tm-30) outliers start: 49 outliers final: 37 residues processed: 256 average time/residue: 1.6776 time to fit residues: 464.1811 Evaluate side-chains 269 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 1.892 ------------------------------------------------------------------------------- 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 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 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 242 ARG 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 D residue 462 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 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 476 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 37 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** 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 = 0.3217 r_free = 0.3217 target = 0.116312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.089246 restraints weight = 16955.740| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.97 r_work: 0.2718 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14654 Z= 0.132 Angle : 0.545 20.061 19813 Z= 0.283 Chirality : 0.042 0.417 2239 Planarity : 0.004 0.046 2394 Dihedral : 7.603 59.128 2336 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.17 % Allowed : 13.20 % Favored : 83.64 % 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: 1.84 (0.21), residues: 1660 helix: 2.65 (0.24), residues: 530 sheet: 0.86 (0.24), residues: 465 loop : 0.39 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 349 HIS 0.005 0.001 HIS C 254 PHE 0.020 0.001 PHE B 92 TYR 0.016 0.002 TYR A 340 ARG 0.002 0.000 ARG D 313 Details of bonding type rmsd link_NAG-ASN : bond 0.01064 ( 10) link_NAG-ASN : angle 5.19563 ( 30) hydrogen bonds : bond 0.06221 ( 689) hydrogen bonds : angle 3.67380 ( 2130) covalent geometry : bond 0.00254 (14644) covalent geometry : angle 0.50698 (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 276 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 227 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.7326 (ttm-80) REVERT: A 269 ASN cc_start: 0.8367 (t0) cc_final: 0.7848 (t0) REVERT: A 308 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.6965 (mtp85) REVERT: A 335 MET cc_start: 0.7623 (mtm) cc_final: 0.6517 (mmp) REVERT: A 345 ASP cc_start: 0.8217 (m-30) cc_final: 0.7853 (m-30) REVERT: A 457 LYS cc_start: 0.7767 (mttt) cc_final: 0.7336 (mtpm) REVERT: B 108 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8157 (mp) REVERT: B 232 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7795 (mtmm) REVERT: B 241 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6434 (mm-30) REVERT: B 269 ASN cc_start: 0.8463 (m-40) cc_final: 0.8149 (m-40) REVERT: B 308 ARG cc_start: 0.7546 (mtm180) cc_final: 0.7232 (mtm110) REVERT: C 82 ASP cc_start: 0.7591 (m-30) cc_final: 0.6383 (p0) REVERT: C 111 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.7879 (mt) REVERT: C 116 MET cc_start: 0.8540 (mtm) cc_final: 0.8004 (mtp) REVERT: C 151 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8206 (mmtp) REVERT: C 179 ARG cc_start: 0.8361 (ttp-170) cc_final: 0.7782 (ttm-80) REVERT: C 181 GLN cc_start: 0.8433 (mm110) cc_final: 0.8134 (mt0) REVERT: C 183 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7602 (p0) REVERT: D 82 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.6037 (p0) REVERT: D 88 MET cc_start: 0.7790 (mtt) cc_final: 0.6833 (mmt) REVERT: D 114 VAL cc_start: 0.7567 (t) cc_final: 0.7192 (p) REVERT: D 165 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8206 (ptt90) REVERT: D 247 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7745 (pt0) REVERT: D 337 ARG cc_start: 0.8005 (mmt180) cc_final: 0.7795 (mmt90) REVERT: D 457 LYS cc_start: 0.7911 (ttmp) cc_final: 0.7101 (ttpt) REVERT: E 106 GLU cc_start: 0.7932 (tt0) cc_final: 0.7409 (tt0) REVERT: E 111 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8033 (mt) REVERT: E 116 MET cc_start: 0.8666 (mtm) cc_final: 0.8335 (mtp) REVERT: E 232 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7341 (mmpt) REVERT: E 269 ASN cc_start: 0.8775 (m-40) cc_final: 0.8390 (m-40) REVERT: E 373 GLU cc_start: 0.6473 (mt-10) cc_final: 0.6190 (tm-30) outliers start: 49 outliers final: 34 residues processed: 260 average time/residue: 1.6491 time to fit residues: 463.4381 Evaluate side-chains 262 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 174 ASP 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 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 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 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 D residue 462 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 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 476 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 159 optimal weight: 0.0370 chunk 1 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 247 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 = 0.3220 r_free = 0.3220 target = 0.116567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.089707 restraints weight = 16936.604| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.96 r_work: 0.2734 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14654 Z= 0.124 Angle : 0.531 19.751 19813 Z= 0.275 Chirality : 0.042 0.419 2239 Planarity : 0.004 0.045 2394 Dihedral : 7.348 59.539 2336 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.85 % Allowed : 13.84 % 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: 1.90 (0.21), residues: 1660 helix: 2.71 (0.24), residues: 530 sheet: 0.87 (0.24), residues: 465 loop : 0.44 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 313 Details of bonding type rmsd link_NAG-ASN : bond 0.01075 ( 10) link_NAG-ASN : angle 5.12043 ( 30) hydrogen bonds : bond 0.05870 ( 689) hydrogen bonds : angle 3.62321 ( 2130) covalent geometry : bond 0.00235 (14644) covalent geometry : angle 0.49237 (19783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11362.82 seconds wall clock time: 196 minutes 30.37 seconds (11790.37 seconds total)