Starting phenix.real_space_refine on Sat Oct 11 12:41:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oq8_17108/10_2025/8oq8_17108.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oq8_17108/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8oq8_17108/10_2025/8oq8_17108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oq8_17108/10_2025/8oq8_17108.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oq8_17108/10_2025/8oq8_17108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oq8_17108/10_2025/8oq8_17108.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 1, 'GLN:plan1': 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: 3.79, per 1000 atoms: 0.26 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: 1.21 Conformation dependent library (CDL) restraints added in 632.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.00 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: 2.70 Time building geometry restraints manager: 1.62 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: 6.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.000 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.630 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (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 ARG 0.020 0.003 ARG C 337 TYR 0.021 0.004 TYR D 219 PHE 0.024 0.004 PHE B 253 TRP 0.017 0.003 TRP A 300 HIS 0.009 0.003 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.01356 (14644) covalent geometry : angle 0.96742 (19783) hydrogen bonds : bond 0.20742 ( 689) hydrogen bonds : angle 5.77573 ( 2130) link_NAG-ASN : bond 0.13151 ( 10) link_NAG-ASN : angle 28.41387 ( 30) *********************** 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 : 0.562 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: 0.7720 time to fit residues: 249.8498 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 : 0.557 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.120047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.093885 restraints weight = 16587.022| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.90 r_work: 0.2733 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14654 Z= 0.146 Angle : 0.620 23.582 19813 Z= 0.313 Chirality : 0.045 0.668 2239 Planarity : 0.004 0.035 2394 Dihedral : 8.412 59.953 2346 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.26 % Allowed : 9.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.21), residues: 1660 helix: 2.50 (0.23), residues: 530 sheet: 1.06 (0.24), residues: 465 loop : 0.64 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 337 TYR 0.021 0.002 TYR E 272 PHE 0.014 0.001 PHE B 92 TRP 0.011 0.001 TRP B 349 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00264 (14644) covalent geometry : angle 0.56031 (19783) hydrogen bonds : bond 0.07406 ( 689) hydrogen bonds : angle 4.25983 ( 2130) link_NAG-ASN : bond 0.00767 ( 10) link_NAG-ASN : angle 6.84575 ( 30) *********************** 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 297 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.379 Fit side-chains REVERT: A 179 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7409 (ttm-80) REVERT: A 269 ASN cc_start: 0.8552 (m110) cc_final: 0.7761 (t0) REVERT: A 335 MET cc_start: 0.7795 (mtm) cc_final: 0.6756 (mmp) REVERT: A 345 ASP cc_start: 0.8304 (m-30) cc_final: 0.7904 (m-30) REVERT: B 151 LYS cc_start: 0.8491 (mmtt) cc_final: 0.7857 (mptt) REVERT: B 241 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6640 (mm-30) REVERT: B 269 ASN cc_start: 0.8444 (m-40) cc_final: 0.8201 (m-40) REVERT: B 278 ARG cc_start: 0.8211 (mtt-85) cc_final: 0.7833 (mtp85) REVERT: B 308 ARG cc_start: 0.7642 (mtm180) cc_final: 0.7320 (mtm110) REVERT: C 82 ASP cc_start: 0.7450 (m-30) cc_final: 0.6081 (p0) REVERT: C 116 MET cc_start: 0.8618 (mtm) cc_final: 0.8058 (mtp) REVERT: C 151 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8081 (mmtp) REVERT: C 179 ARG cc_start: 0.8441 (ttp-170) cc_final: 0.7895 (ttm-80) REVERT: C 235 ASP cc_start: 0.8222 (m-30) cc_final: 0.7965 (m-30) REVERT: D 113 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7892 (mt-10) REVERT: D 114 VAL cc_start: 0.7642 (t) cc_final: 0.7337 (p) REVERT: D 179 ARG cc_start: 0.8116 (ttp-170) cc_final: 0.7663 (ttp-170) REVERT: D 239 THR cc_start: 0.8715 (p) cc_final: 0.8515 (m) REVERT: E 106 GLU cc_start: 0.7991 (tt0) cc_final: 0.7399 (tt0) REVERT: E 116 MET cc_start: 0.8672 (mtm) cc_final: 0.8423 (mtp) REVERT: E 232 LYS cc_start: 0.8351 (mtmm) cc_final: 0.7416 (mmtt) REVERT: E 269 ASN cc_start: 0.8730 (m-40) cc_final: 0.8264 (t0) REVERT: E 372 GLN cc_start: 0.7848 (tp40) cc_final: 0.7645 (mm-40) REVERT: E 373 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6574 (tm-30) REVERT: E 375 LYS cc_start: 0.6409 (tmtt) cc_final: 0.6162 (tmtt) outliers start: 35 outliers final: 14 residues processed: 275 average time/residue: 0.7251 time to fit residues: 215.2807 Evaluate side-chains 258 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 244 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 265 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain 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 81 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3173 r_free = 0.3173 target = 0.113051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.086140 restraints weight = 16834.117| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 1.93 r_work: 0.2653 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14654 Z= 0.221 Angle : 0.718 22.307 19813 Z= 0.371 Chirality : 0.048 0.538 2239 Planarity : 0.005 0.049 2394 Dihedral : 8.998 59.911 2337 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.75 % Allowed : 9.70 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.20), residues: 1660 helix: 1.90 (0.23), residues: 565 sheet: 0.65 (0.24), residues: 440 loop : 0.31 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 337 TYR 0.018 0.002 TYR B 123 PHE 0.016 0.002 PHE B 92 TRP 0.010 0.002 TRP B 349 HIS 0.006 0.002 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00499 (14644) covalent geometry : angle 0.66716 (19783) hydrogen bonds : bond 0.08958 ( 689) hydrogen bonds : angle 4.22634 ( 2130) link_NAG-ASN : bond 0.00827 ( 10) link_NAG-ASN : angle 6.84878 ( 30) *********************** 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 293 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8434 (ttp-170) cc_final: 0.7519 (ttm-80) REVERT: A 227 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.6947 (tmt) REVERT: A 269 ASN cc_start: 0.8608 (m110) cc_final: 0.7670 (t0) REVERT: A 335 MET cc_start: 0.7882 (mtm) cc_final: 0.6797 (mmp) REVERT: A 337 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6834 (mtm-85) REVERT: A 345 ASP cc_start: 0.8371 (m-30) cc_final: 0.7984 (m-30) REVERT: B 158 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8713 (mpm) REVERT: B 197 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8199 (ptp) REVERT: B 241 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6626 (mm-30) REVERT: B 269 ASN cc_start: 0.8624 (m-40) cc_final: 0.8227 (m-40) REVERT: B 308 ARG cc_start: 0.7691 (mtm180) cc_final: 0.7381 (mtm110) REVERT: B 337 ARG cc_start: 0.7825 (ttm-80) cc_final: 0.7594 (tpp-160) REVERT: C 82 ASP cc_start: 0.7594 (m-30) cc_final: 0.6275 (p0) REVERT: C 88 MET cc_start: 0.8198 (ptp) cc_final: 0.7940 (ptt) REVERT: C 116 MET cc_start: 0.8695 (mtm) cc_final: 0.8308 (mtp) REVERT: C 151 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8214 (mmtp) REVERT: C 179 ARG cc_start: 0.8498 (ttp-170) cc_final: 0.7935 (ttm-80) REVERT: D 82 ASP cc_start: 0.6528 (OUTLIER) cc_final: 0.6117 (OUTLIER) REVERT: D 114 VAL cc_start: 0.7745 (t) cc_final: 0.7390 (p) REVERT: D 179 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.7736 (ttp-170) REVERT: D 457 LYS cc_start: 0.8135 (ttmp) cc_final: 0.7346 (ttpt) REVERT: E 106 GLU cc_start: 0.8027 (tt0) cc_final: 0.7436 (tt0) REVERT: E 111 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8099 (mt) REVERT: E 116 MET cc_start: 0.8805 (mtm) cc_final: 0.8545 (mtp) REVERT: E 232 LYS cc_start: 0.8269 (mtmm) cc_final: 0.7475 (mmpt) REVERT: E 269 ASN cc_start: 0.8865 (m-40) cc_final: 0.8280 (t0) REVERT: E 373 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6488 (tm-30) REVERT: E 375 LYS cc_start: 0.6458 (OUTLIER) cc_final: 0.6223 (tmtt) outliers start: 58 outliers final: 29 residues processed: 272 average time/residue: 0.7333 time to fit residues: 215.6409 Evaluate side-chains 265 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 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 251 GLN 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 250 ILE Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 375 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 139 ASN 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 = 0.3230 r_free = 0.3230 target = 0.117001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.090989 restraints weight = 16761.749| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.87 r_work: 0.2694 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1670 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= 0.166 Angle : 0.624 20.758 19813 Z= 0.322 Chirality : 0.045 0.494 2239 Planarity : 0.004 0.048 2394 Dihedral : 8.737 59.342 2337 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.36 % Allowed : 11.32 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.20), residues: 1660 helix: 1.99 (0.23), residues: 565 sheet: 0.63 (0.24), residues: 440 loop : 0.26 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 337 TYR 0.016 0.002 TYR B 272 PHE 0.016 0.002 PHE B 92 TRP 0.011 0.001 TRP B 349 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00342 (14644) covalent geometry : angle 0.57691 (19783) hydrogen bonds : bond 0.07574 ( 689) hydrogen bonds : angle 3.98262 ( 2130) link_NAG-ASN : bond 0.00996 ( 10) link_NAG-ASN : angle 6.12357 ( 30) *********************** 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 278 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 226 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.7584 (ttm-80) REVERT: A 227 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.6956 (tmt) REVERT: A 269 ASN cc_start: 0.8539 (m110) cc_final: 0.7712 (t0) REVERT: A 308 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7148 (mtp85) REVERT: A 335 MET cc_start: 0.7868 (mtm) cc_final: 0.6834 (mmp) REVERT: A 345 ASP cc_start: 0.8308 (m-30) cc_final: 0.7925 (m-30) REVERT: B 158 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8746 (mpm) REVERT: B 241 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6585 (mm-30) REVERT: B 269 ASN cc_start: 0.8548 (m-40) cc_final: 0.8236 (m-40) REVERT: B 308 ARG cc_start: 0.7733 (mtm180) cc_final: 0.7433 (mtm110) REVERT: C 82 ASP cc_start: 0.7526 (m-30) cc_final: 0.6284 (p0) REVERT: C 116 MET cc_start: 0.8723 (mtm) cc_final: 0.8191 (mtp) REVERT: C 151 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8121 (mmtp) REVERT: C 179 ARG cc_start: 0.8455 (ttp-170) cc_final: 0.7964 (ttm-80) REVERT: C 223 GLU cc_start: 0.7911 (tp30) cc_final: 0.7653 (mm-30) REVERT: D 114 VAL cc_start: 0.7760 (t) cc_final: 0.7413 (p) REVERT: D 165 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8254 (ptt90) REVERT: D 179 ARG cc_start: 0.8160 (ttp-170) cc_final: 0.7760 (ttp-170) REVERT: D 457 LYS cc_start: 0.8159 (ttmp) cc_final: 0.7416 (ttpt) REVERT: E 106 GLU cc_start: 0.7954 (tt0) cc_final: 0.7387 (tt0) REVERT: E 111 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8127 (mt) REVERT: E 116 MET cc_start: 0.8786 (mtm) cc_final: 0.8468 (mtp) REVERT: E 232 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7507 (mmpt) REVERT: E 269 ASN cc_start: 0.8780 (m-40) cc_final: 0.8394 (m-40) REVERT: E 373 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6539 (tm-30) REVERT: E 375 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.6305 (tmtt) outliers start: 52 outliers final: 30 residues processed: 265 average time/residue: 0.7344 time to fit residues: 209.9811 Evaluate side-chains 258 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain 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 310 VAL Chi-restraints excluded: chain B residue 335 MET 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 265 THR Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER 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 287 GLN Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 375 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 161 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 247 GLN C 287 GLN C 372 GLN D 251 GLN E 247 GLN E 251 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.111166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.084332 restraints weight = 17025.797| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.95 r_work: 0.2661 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 14654 Z= 0.204 Angle : 0.678 20.539 19813 Z= 0.352 Chirality : 0.046 0.462 2239 Planarity : 0.005 0.052 2394 Dihedral : 9.090 59.730 2337 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.33 % Allowed : 11.32 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.20), residues: 1660 helix: 2.27 (0.23), residues: 535 sheet: 0.71 (0.24), residues: 465 loop : 0.15 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 165 TYR 0.017 0.002 TYR B 123 PHE 0.017 0.002 PHE B 92 TRP 0.011 0.002 TRP C 128 HIS 0.006 0.002 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00452 (14644) covalent geometry : angle 0.63612 (19783) hydrogen bonds : bond 0.08407 ( 689) hydrogen bonds : angle 4.02605 ( 2130) link_NAG-ASN : bond 0.01053 ( 10) link_NAG-ASN : angle 6.03265 ( 30) *********************** 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 297 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 230 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8398 (ttp-170) cc_final: 0.7478 (ttm-80) REVERT: A 181 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8090 (mm110) REVERT: A 227 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.6835 (tmt) REVERT: A 269 ASN cc_start: 0.8567 (m110) cc_final: 0.7667 (t0) REVERT: A 308 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7067 (mtp85) REVERT: A 335 MET cc_start: 0.7820 (mtm) cc_final: 0.6663 (mmp) REVERT: A 337 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6861 (mtm-85) REVERT: A 345 ASP cc_start: 0.8340 (m-30) cc_final: 0.7935 (m-30) REVERT: A 457 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7498 (mtpm) REVERT: B 158 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8717 (mpm) REVERT: B 241 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6593 (mm-30) REVERT: B 269 ASN cc_start: 0.8598 (m-40) cc_final: 0.8193 (m-40) REVERT: B 308 ARG cc_start: 0.7623 (mtm180) cc_final: 0.7314 (mtm110) REVERT: C 82 ASP cc_start: 0.7564 (m-30) cc_final: 0.6311 (p0) REVERT: C 92 PHE cc_start: 0.8254 (t80) cc_final: 0.7963 (t80) REVERT: C 111 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.7908 (mt) REVERT: C 116 MET cc_start: 0.8665 (mtm) cc_final: 0.8138 (mtp) REVERT: C 151 LYS cc_start: 0.8476 (mmtt) cc_final: 0.8226 (mmtp) REVERT: C 179 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.7870 (ttm-80) REVERT: C 181 GLN cc_start: 0.8504 (mm110) cc_final: 0.8222 (mt0) REVERT: C 183 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7744 (p0) REVERT: C 223 GLU cc_start: 0.7875 (tp30) cc_final: 0.7565 (mm-30) REVERT: D 82 ASP cc_start: 0.6527 (OUTLIER) cc_final: 0.6062 (OUTLIER) REVERT: D 114 VAL cc_start: 0.7701 (t) cc_final: 0.7314 (p) REVERT: D 165 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8269 (ptt90) REVERT: D 179 ARG cc_start: 0.8175 (ttp-170) cc_final: 0.7685 (ttp-170) REVERT: D 247 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7708 (pt0) REVERT: D 457 LYS cc_start: 0.8095 (ttmp) cc_final: 0.7309 (ttpt) REVERT: E 106 GLU cc_start: 0.7971 (tt0) cc_final: 0.7410 (tt0) REVERT: E 111 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8053 (mt) REVERT: E 116 MET cc_start: 0.8799 (mtm) cc_final: 0.8473 (mtp) REVERT: E 232 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7427 (mmpt) REVERT: E 269 ASN cc_start: 0.8864 (m-40) cc_final: 0.8382 (m-40) REVERT: E 373 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6439 (tm-30) REVERT: E 375 LYS cc_start: 0.6421 (OUTLIER) cc_final: 0.6202 (tmtt) outliers start: 67 outliers final: 44 residues processed: 273 average time/residue: 0.7214 time to fit residues: 212.8722 Evaluate side-chains 281 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 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 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 337 ARG Chi-restraints excluded: chain A residue 457 LYS 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 335 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 375 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 160 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 247 GLN C 251 GLN C 372 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3170 r_free = 0.3170 target = 0.112720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.085929 restraints weight = 17042.339| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.95 r_work: 0.2676 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1814 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= 0.162 Angle : 0.616 20.214 19813 Z= 0.319 Chirality : 0.044 0.471 2239 Planarity : 0.004 0.049 2394 Dihedral : 8.784 59.550 2337 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.20 % Allowed : 11.90 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.21), residues: 1660 helix: 2.37 (0.23), residues: 535 sheet: 0.72 (0.24), residues: 465 loop : 0.17 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 191 TYR 0.016 0.002 TYR E 272 PHE 0.018 0.002 PHE B 92 TRP 0.012 0.001 TRP B 349 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00329 (14644) covalent geometry : angle 0.57218 (19783) hydrogen bonds : bond 0.07461 ( 689) hydrogen bonds : angle 3.90371 ( 2130) link_NAG-ASN : bond 0.01140 ( 10) link_NAG-ASN : angle 5.91890 ( 30) *********************** 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 289 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 224 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8325 (ttp-170) cc_final: 0.7433 (ttm-80) REVERT: A 181 GLN cc_start: 0.8259 (mm-40) cc_final: 0.8038 (mm110) REVERT: A 227 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.6819 (tmt) REVERT: A 269 ASN cc_start: 0.8536 (m110) cc_final: 0.7665 (t0) REVERT: A 308 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7020 (mtp85) REVERT: A 335 MET cc_start: 0.7745 (mtm) cc_final: 0.6659 (mmp) REVERT: A 337 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6802 (mtm-85) REVERT: A 345 ASP cc_start: 0.8283 (m-30) cc_final: 0.7900 (m-30) REVERT: A 457 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7443 (mtpm) REVERT: B 158 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8726 (mpm) REVERT: B 241 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6579 (mm-30) REVERT: B 269 ASN cc_start: 0.8571 (m-40) cc_final: 0.8206 (m-40) REVERT: B 308 ARG cc_start: 0.7611 (mtm180) cc_final: 0.7310 (mtm110) REVERT: C 82 ASP cc_start: 0.7560 (m-30) cc_final: 0.6348 (p0) REVERT: C 92 PHE cc_start: 0.8252 (t80) cc_final: 0.7976 (t80) REVERT: C 111 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.7900 (mt) REVERT: C 116 MET cc_start: 0.8590 (mtm) cc_final: 0.8067 (mtp) REVERT: C 151 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8009 (mmtp) REVERT: C 179 ARG cc_start: 0.8405 (ttp-170) cc_final: 0.7841 (ttm-80) REVERT: C 181 GLN cc_start: 0.8478 (mm110) cc_final: 0.8192 (mt0) REVERT: C 183 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7690 (p0) REVERT: C 223 GLU cc_start: 0.7841 (tp30) cc_final: 0.7495 (mm-30) REVERT: D 114 VAL cc_start: 0.7622 (t) cc_final: 0.7247 (p) REVERT: D 165 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8237 (ptt90) REVERT: D 179 ARG cc_start: 0.8120 (ttp-170) cc_final: 0.7624 (ttp-170) REVERT: D 239 THR cc_start: 0.8737 (p) cc_final: 0.8506 (m) REVERT: D 247 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7749 (pt0) REVERT: D 457 LYS cc_start: 0.8055 (ttmp) cc_final: 0.7275 (ttpt) REVERT: E 106 GLU cc_start: 0.7950 (tt0) cc_final: 0.7389 (tt0) REVERT: E 111 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8051 (mt) REVERT: E 116 MET cc_start: 0.8727 (mtm) cc_final: 0.8395 (mtp) REVERT: E 232 LYS cc_start: 0.8150 (mtmm) cc_final: 0.7401 (mmpt) REVERT: E 269 ASN cc_start: 0.8813 (m-40) cc_final: 0.8362 (m-40) REVERT: E 373 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6260 (tm-30) REVERT: E 375 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.6214 (tmtt) outliers start: 65 outliers final: 40 residues processed: 266 average time/residue: 0.7546 time to fit residues: 216.1672 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 : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 256 THR 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 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 337 ARG Chi-restraints excluded: chain A residue 457 LYS 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 310 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 265 THR 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 247 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 375 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 118 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 147 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 287 GLN B 247 GLN C 372 GLN D 251 GLN E 247 GLN E 251 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.115208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.088438 restraints weight = 16866.857| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.94 r_work: 0.2709 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14654 Z= 0.134 Angle : 0.559 20.297 19813 Z= 0.289 Chirality : 0.043 0.437 2239 Planarity : 0.004 0.048 2394 Dihedral : 8.292 58.571 2337 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.49 % Allowed : 12.68 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.21), residues: 1660 helix: 2.56 (0.24), residues: 530 sheet: 0.78 (0.24), residues: 465 loop : 0.25 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 191 TYR 0.016 0.002 TYR A 340 PHE 0.018 0.001 PHE B 92 TRP 0.012 0.001 TRP B 349 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00254 (14644) covalent geometry : angle 0.51648 (19783) hydrogen bonds : bond 0.06542 ( 689) hydrogen bonds : angle 3.76184 ( 2130) link_NAG-ASN : bond 0.01047 ( 10) link_NAG-ASN : angle 5.53208 ( 30) *********************** 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 283 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8228 (ttp-170) cc_final: 0.7327 (ttm-80) REVERT: A 181 GLN cc_start: 0.8263 (mm-40) cc_final: 0.8043 (mm110) REVERT: A 227 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.6823 (tmt) REVERT: A 308 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7026 (mtp85) REVERT: A 335 MET cc_start: 0.7673 (mtm) cc_final: 0.6606 (mmp) REVERT: A 337 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6754 (mtm-85) REVERT: A 345 ASP cc_start: 0.8254 (m-30) cc_final: 0.7882 (m-30) REVERT: A 457 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7422 (mtpm) REVERT: B 232 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7805 (mtmm) REVERT: B 241 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6541 (mm-30) REVERT: B 269 ASN cc_start: 0.8486 (m-40) cc_final: 0.8172 (m-40) REVERT: B 308 ARG cc_start: 0.7575 (mtm180) cc_final: 0.7274 (mtm110) REVERT: C 82 ASP cc_start: 0.7569 (m-30) cc_final: 0.6373 (p0) REVERT: C 92 PHE cc_start: 0.8270 (t80) cc_final: 0.8015 (t80) REVERT: C 111 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.7869 (mt) REVERT: C 116 MET cc_start: 0.8553 (mtm) cc_final: 0.8146 (mtp) REVERT: C 151 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8039 (mmtp) REVERT: C 179 ARG cc_start: 0.8357 (ttp-170) cc_final: 0.7812 (ttm-80) REVERT: C 181 GLN cc_start: 0.8452 (mm110) cc_final: 0.8168 (mt0) REVERT: C 183 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7624 (p0) REVERT: C 223 GLU cc_start: 0.7833 (tp30) cc_final: 0.7518 (mm-30) REVERT: D 114 VAL cc_start: 0.7605 (t) cc_final: 0.7244 (p) REVERT: D 179 ARG cc_start: 0.8052 (ttp-170) cc_final: 0.7574 (ttp-170) REVERT: D 247 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: D 457 LYS cc_start: 0.8008 (ttmp) cc_final: 0.7216 (ttpt) REVERT: E 106 GLU cc_start: 0.7946 (tt0) cc_final: 0.7436 (tt0) REVERT: E 111 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8061 (mt) REVERT: E 116 MET cc_start: 0.8701 (mtm) cc_final: 0.8373 (mtp) REVERT: E 232 LYS cc_start: 0.8153 (mtmm) cc_final: 0.7422 (mmpt) REVERT: E 269 ASN cc_start: 0.8769 (m-40) cc_final: 0.8381 (m-40) REVERT: E 373 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6246 (tm-30) outliers start: 54 outliers final: 34 residues processed: 264 average time/residue: 0.7648 time to fit residues: 217.7484 Evaluate side-chains 266 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 337 ARG 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 122 LEU 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 247 GLN Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 59 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 269 ASN A 287 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.113144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.086345 restraints weight = 16929.059| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.95 r_work: 0.2682 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14654 Z= 0.161 Angle : 0.600 20.038 19813 Z= 0.312 Chirality : 0.044 0.441 2239 Planarity : 0.004 0.047 2394 Dihedral : 8.315 58.088 2336 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.56 % Allowed : 12.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.21), residues: 1660 helix: 2.46 (0.23), residues: 535 sheet: 0.76 (0.24), residues: 465 loop : 0.22 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 242 TYR 0.015 0.002 TYR A 340 PHE 0.019 0.002 PHE B 92 TRP 0.011 0.001 TRP C 128 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00336 (14644) covalent geometry : angle 0.56232 (19783) hydrogen bonds : bond 0.07190 ( 689) hydrogen bonds : angle 3.79459 ( 2130) link_NAG-ASN : bond 0.01107 ( 10) link_NAG-ASN : angle 5.39972 ( 30) *********************** 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 281 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7340 (ttm-80) REVERT: A 181 GLN cc_start: 0.8239 (mm-40) cc_final: 0.8014 (mm110) REVERT: A 227 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.6831 (tmt) REVERT: A 308 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.6998 (mtp85) REVERT: A 335 MET cc_start: 0.7707 (mtm) cc_final: 0.6635 (mmp) REVERT: A 337 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6775 (mtm-85) REVERT: A 345 ASP cc_start: 0.8288 (m-30) cc_final: 0.7911 (m-30) REVERT: A 457 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7424 (mtpm) REVERT: B 232 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7791 (mtmm) REVERT: B 241 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6572 (mm-30) REVERT: B 269 ASN cc_start: 0.8525 (m-40) cc_final: 0.8176 (m-40) REVERT: B 308 ARG cc_start: 0.7600 (mtm180) cc_final: 0.7297 (mtm110) REVERT: C 82 ASP cc_start: 0.7556 (m-30) cc_final: 0.6339 (p0) REVERT: C 92 PHE cc_start: 0.8266 (t80) cc_final: 0.7999 (t80) REVERT: C 111 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.7894 (mt) REVERT: C 116 MET cc_start: 0.8591 (mtm) cc_final: 0.8057 (mtp) REVERT: C 151 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8010 (mmtp) REVERT: C 179 ARG cc_start: 0.8402 (ttp-170) cc_final: 0.7839 (ttm-80) REVERT: C 183 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7650 (p0) REVERT: C 223 GLU cc_start: 0.7827 (tp30) cc_final: 0.7498 (mm-30) REVERT: D 88 MET cc_start: 0.7856 (mtt) cc_final: 0.6870 (mmt) REVERT: D 114 VAL cc_start: 0.7620 (t) cc_final: 0.7243 (p) REVERT: D 165 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8226 (ptt90) REVERT: D 337 ARG cc_start: 0.8011 (mmt180) cc_final: 0.7792 (mmt90) REVERT: D 457 LYS cc_start: 0.8084 (ttmp) cc_final: 0.7264 (tttt) REVERT: E 106 GLU cc_start: 0.7961 (tt0) cc_final: 0.7435 (tt0) REVERT: E 111 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8064 (mt) REVERT: E 116 MET cc_start: 0.8717 (mtm) cc_final: 0.8388 (mtp) REVERT: E 232 LYS cc_start: 0.8137 (mtmm) cc_final: 0.7396 (mmpt) REVERT: E 269 ASN cc_start: 0.8816 (m-40) cc_final: 0.8375 (m-40) REVERT: E 373 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6243 (tm-30) outliers start: 55 outliers final: 39 residues processed: 263 average time/residue: 0.7303 time to fit residues: 207.4176 Evaluate side-chains 272 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 337 ARG 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 265 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 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 287 GLN Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 36 optimal weight: 0.8980 chunk 122 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 1 optimal weight: 0.0570 chunk 90 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 247 GLN C 251 GLN C 372 GLN D 251 GLN E 247 GLN E 251 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.115558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.088681 restraints weight = 17012.553| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.96 r_work: 0.2710 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14654 Z= 0.136 Angle : 0.579 20.759 19813 Z= 0.297 Chirality : 0.042 0.356 2239 Planarity : 0.004 0.046 2394 Dihedral : 8.012 57.708 2336 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.98 % Allowed : 13.52 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.21), residues: 1660 helix: 2.61 (0.24), residues: 530 sheet: 0.80 (0.24), residues: 465 loop : 0.29 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 242 TYR 0.016 0.002 TYR A 340 PHE 0.020 0.001 PHE B 92 TRP 0.012 0.001 TRP B 349 HIS 0.004 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00258 (14644) covalent geometry : angle 0.52798 (19783) hydrogen bonds : bond 0.06438 ( 689) hydrogen bonds : angle 3.71813 ( 2130) link_NAG-ASN : bond 0.01106 ( 10) link_NAG-ASN : angle 6.13691 ( 30) *********************** 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: 46 poor density : 225 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8234 (ttp-170) cc_final: 0.7352 (ttm-80) REVERT: A 308 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6964 (mtp85) REVERT: A 335 MET cc_start: 0.7691 (mtm) cc_final: 0.6582 (mmp) REVERT: A 337 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6703 (mtm-85) REVERT: A 345 ASP cc_start: 0.8245 (m-30) cc_final: 0.7878 (m-30) REVERT: A 457 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7386 (mtpm) REVERT: B 232 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7787 (mtmm) REVERT: B 241 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6455 (mm-30) REVERT: B 269 ASN cc_start: 0.8472 (m-40) cc_final: 0.8162 (m-40) REVERT: B 308 ARG cc_start: 0.7566 (mtm180) cc_final: 0.7261 (mtm110) REVERT: C 82 ASP cc_start: 0.7579 (m-30) cc_final: 0.6377 (p0) REVERT: C 92 PHE cc_start: 0.8274 (t80) cc_final: 0.8010 (t80) REVERT: C 111 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.7881 (mt) REVERT: C 116 MET cc_start: 0.8543 (mtm) cc_final: 0.8131 (mtp) REVERT: C 151 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8052 (mmtp) REVERT: C 179 ARG cc_start: 0.8350 (ttp-170) cc_final: 0.7802 (ttm-80) REVERT: C 183 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7616 (p0) REVERT: C 223 GLU cc_start: 0.7806 (tp30) cc_final: 0.7479 (mm-30) REVERT: C 345 ASP cc_start: 0.8392 (m-30) cc_final: 0.8162 (m-30) REVERT: D 88 MET cc_start: 0.7859 (mtt) cc_final: 0.6880 (mmt) REVERT: D 114 VAL cc_start: 0.7561 (t) cc_final: 0.7190 (p) REVERT: D 165 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8180 (ptt90) REVERT: D 337 ARG cc_start: 0.8008 (mmt180) cc_final: 0.7787 (mmt90) REVERT: D 457 LYS cc_start: 0.8014 (ttmp) cc_final: 0.7235 (ttpt) REVERT: E 106 GLU cc_start: 0.7940 (tt0) cc_final: 0.7421 (tt0) REVERT: E 111 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8060 (mt) REVERT: E 116 MET cc_start: 0.8674 (mtm) cc_final: 0.8347 (mtp) REVERT: E 232 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7382 (mmpt) REVERT: E 269 ASN cc_start: 0.8789 (m-40) cc_final: 0.8387 (m-40) REVERT: E 373 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6225 (tm-30) outliers start: 46 outliers final: 33 residues processed: 256 average time/residue: 0.7427 time to fit residues: 204.9718 Evaluate side-chains 261 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 224 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 337 ARG 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 122 LEU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 165 ARG 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 287 GLN Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 247 GLN C 251 GLN C 372 GLN E 247 GLN E 251 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.112362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.085509 restraints weight = 16856.301| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.94 r_work: 0.2670 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14654 Z= 0.179 Angle : 0.636 20.650 19813 Z= 0.331 Chirality : 0.045 0.370 2239 Planarity : 0.004 0.048 2394 Dihedral : 8.479 59.828 2336 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.43 % Allowed : 13.32 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.21), residues: 1660 helix: 2.44 (0.23), residues: 535 sheet: 0.74 (0.24), residues: 465 loop : 0.18 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 374 TYR 0.015 0.002 TYR E 272 PHE 0.020 0.002 PHE B 92 TRP 0.010 0.001 TRP C 128 HIS 0.006 0.002 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00386 (14644) covalent geometry : angle 0.59555 (19783) hydrogen bonds : bond 0.07663 ( 689) hydrogen bonds : angle 3.85479 ( 2130) link_NAG-ASN : bond 0.01112 ( 10) link_NAG-ASN : angle 5.75971 ( 30) ********************** 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 277 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 224 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8310 (ttp-170) cc_final: 0.7369 (ttm-80) REVERT: A 269 ASN cc_start: 0.8427 (t0) cc_final: 0.7940 (t0) REVERT: A 308 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7008 (mtp85) REVERT: A 335 MET cc_start: 0.7748 (mtm) cc_final: 0.6673 (mmp) REVERT: A 337 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6773 (mtm-85) REVERT: A 345 ASP cc_start: 0.8321 (m-30) cc_final: 0.7933 (m-30) REVERT: A 457 LYS cc_start: 0.7885 (mttt) cc_final: 0.7444 (mtpm) REVERT: B 269 ASN cc_start: 0.8577 (m-40) cc_final: 0.8198 (m-40) REVERT: B 308 ARG cc_start: 0.7600 (mtm180) cc_final: 0.7294 (mtm110) REVERT: C 82 ASP cc_start: 0.7606 (m-30) cc_final: 0.6399 (p0) REVERT: C 92 PHE cc_start: 0.8249 (t80) cc_final: 0.8021 (t80) REVERT: C 111 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.7910 (mt) REVERT: C 116 MET cc_start: 0.8632 (mtm) cc_final: 0.8107 (mtp) REVERT: C 151 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8013 (mmtp) REVERT: C 179 ARG cc_start: 0.8394 (ttp-170) cc_final: 0.7846 (ttm-80) REVERT: C 183 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7685 (p0) REVERT: C 223 GLU cc_start: 0.7841 (tp30) cc_final: 0.7557 (mm-30) REVERT: D 88 MET cc_start: 0.7843 (mtt) cc_final: 0.6880 (mmt) REVERT: D 114 VAL cc_start: 0.7641 (t) cc_final: 0.7266 (p) REVERT: D 165 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8215 (ptt90) REVERT: D 337 ARG cc_start: 0.7988 (mmt180) cc_final: 0.7767 (mmt90) REVERT: D 457 LYS cc_start: 0.8078 (ttmp) cc_final: 0.7301 (ttpt) REVERT: E 106 GLU cc_start: 0.7967 (tt0) cc_final: 0.7438 (tt0) REVERT: E 111 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8063 (mt) REVERT: E 116 MET cc_start: 0.8749 (mtm) cc_final: 0.8417 (mtp) REVERT: E 232 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7388 (mmtt) REVERT: E 269 ASN cc_start: 0.8843 (m-40) cc_final: 0.8365 (m-40) REVERT: E 373 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6272 (tm-30) outliers start: 53 outliers final: 39 residues processed: 262 average time/residue: 0.7214 time to fit residues: 204.2552 Evaluate side-chains 269 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 165 ARG 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 287 GLN Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 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 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 = 0.3170 r_free = 0.3170 target = 0.112602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.085664 restraints weight = 16981.800| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.95 r_work: 0.2669 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 14654 Z= 0.188 Angle : 0.828 59.200 19813 Z= 0.471 Chirality : 0.044 0.374 2239 Planarity : 0.004 0.048 2394 Dihedral : 8.471 59.777 2336 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.36 % Allowed : 13.39 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.21), residues: 1660 helix: 2.44 (0.23), residues: 535 sheet: 0.73 (0.24), residues: 465 loop : 0.17 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 374 TYR 0.015 0.002 TYR A 340 PHE 0.018 0.002 PHE B 92 TRP 0.010 0.001 TRP C 128 HIS 0.005 0.002 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00371 (14644) covalent geometry : angle 0.79831 (19783) hydrogen bonds : bond 0.07519 ( 689) hydrogen bonds : angle 3.85403 ( 2130) link_NAG-ASN : bond 0.01088 ( 10) link_NAG-ASN : angle 5.74920 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5376.37 seconds wall clock time: 92 minutes 20.44 seconds (5540.44 seconds total)