Starting phenix.real_space_refine on Fri May 16 09:04:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rh4_19167/05_2025/8rh4_19167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rh4_19167/05_2025/8rh4_19167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rh4_19167/05_2025/8rh4_19167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rh4_19167/05_2025/8rh4_19167.map" model { file = "/net/cci-nas-00/data/ceres_data/8rh4_19167/05_2025/8rh4_19167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rh4_19167/05_2025/8rh4_19167.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 75 5.16 5 Cl 2 4.86 5 C 9430 2.51 5 N 2220 2.21 5 O 2565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14292 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2741 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Chain: "E" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2741 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Chain: "C" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2741 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 139 Unusual residues: {' CL': 1, 'D10': 1, 'EST': 2, 'HEX': 6, 'NAG': 2, 'OCT': 3} Classifications: {'undetermined': 15} Link IDs: {None: 14} 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: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 92 Unusual residues: {'D10': 1, 'HEX': 5, 'NAG': 2, 'OCT': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 107 Unusual residues: {' CL': 1, 'D10': 1, 'EST': 1, 'HEX': 4, 'NAG': 2, 'OCT': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 112 Unusual residues: {'D10': 1, 'EST': 1, 'HEX': 5, 'NAG': 2, 'OCT': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 112 Unusual residues: {'D10': 1, 'EST': 1, 'HEX': 5, 'NAG': 2, 'OCT': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Restraints were copied for chains: B, D Time building chain proxies: 10.89, per 1000 atoms: 0.76 Number of scatterers: 14292 At special positions: 0 Unit cell: (92.805, 93.4775, 133.155, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 75 16.00 O 2565 8.00 N 2220 7.00 C 9430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 212 " distance=2.04 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 198 " distance=0.00 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 198 " distance=2.04 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 212 " distance=0.00 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 212 " distance=2.04 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 "HETATM13862 O5 NAG E 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM13717 O5 NAG A 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM13948 O5 NAG B 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM14061 O5 NAG C 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14199 O5 NAG D 504 .*. 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 501 " - " ASN B 140 " " NAG B 502 " - " ASN B 234 " " NAG C 502 " - " ASN C 140 " " NAG C 503 " - " ASN C 234 " " NAG D 504 " - " ASN D 140 " " NAG D 505 " - " ASN D 234 " " NAG E 502 " - " ASN E 140 " " NAG E 503 " - " ASN E 234 " Time building additional restraints: 3.88 Conformation dependent library (CDL) restraints added in 1.9 seconds 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 40.7% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.988A pdb=" N HIS A 84 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 146 through 151 removed outlier: 3.961A pdb=" N VAL A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 151' Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.935A pdb=" N PHE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.605A pdb=" N TRP A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 335 Proline residue: A 315 - end of helix removed outlier: 3.704A pdb=" N ILE A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 377 removed outlier: 3.691A pdb=" N TYR A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 479 removed outlier: 4.193A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.988A pdb=" N HIS E 84 " --> pdb=" O ILE E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 146 through 151 removed outlier: 3.960A pdb=" N VAL E 150 " --> pdb=" O ASP E 146 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 151' Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 280 through 301 removed outlier: 3.936A pdb=" N PHE E 284 " --> pdb=" O HIS E 280 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.606A pdb=" N TRP E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL E 301 " --> pdb=" O MET E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 335 Proline residue: E 315 - end of helix removed outlier: 3.704A pdb=" N ILE E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 377 removed outlier: 3.691A pdb=" N TYR E 347 " --> pdb=" O ALA E 343 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR E 362 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 363 " --> pdb=" O VAL E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 479 removed outlier: 4.193A pdb=" N ILE E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.988A pdb=" N HIS B 84 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.961A pdb=" N VAL B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 151' Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.936A pdb=" N PHE B 284 " --> pdb=" O HIS B 280 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.606A pdb=" N TRP B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 335 Proline residue: B 315 - end of helix removed outlier: 3.705A pdb=" N ILE B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 377 removed outlier: 3.691A pdb=" N TYR B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 363 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 479 removed outlier: 4.192A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.988A 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 151 removed outlier: 3.961A pdb=" N VAL C 150 " --> pdb=" O ASP C 146 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 151' Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.936A pdb=" N PHE C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.606A pdb=" N TRP C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 335 Proline residue: C 315 - end of helix removed outlier: 3.704A pdb=" N ILE C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 377 removed outlier: 3.691A pdb=" N TYR C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 363 " --> pdb=" O VAL C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 479 removed outlier: 4.192A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Proline residue: C 464 - end of helix Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.987A pdb=" N HIS D 84 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 146 through 151 removed outlier: 3.961A pdb=" N VAL D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 151' Processing helix chain 'D' and resid 232 through 235 Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.935A pdb=" N PHE D 284 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.605A pdb=" N TRP D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL D 301 " --> pdb=" O MET D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 335 Proline residue: D 315 - end of helix removed outlier: 3.704A pdb=" N ILE D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 377 removed outlier: 3.692A pdb=" N TYR D 347 " --> pdb=" O ALA D 343 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 363 " --> pdb=" O VAL D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 479 removed outlier: 4.193A pdb=" N ILE D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Proline residue: D 464 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 145 removed outlier: 3.703A pdb=" N SER A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A 121 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU A 108 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR A 123 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU A 106 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ARG A 125 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLN A 104 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR A 127 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASP A 102 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N LYS A 129 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLY A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 removed outlier: 7.083A pdb=" N SER A 163 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET A 197 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 165 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A 121 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU A 108 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR A 123 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU A 106 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ARG A 125 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLN A 104 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR A 127 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASP A 102 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N LYS A 129 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLY A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.650A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N SER A 218 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASN A 269 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR A 276 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU A 252 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ARG A 278 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE A 250 " --> pdb=" O ARG A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 143 through 145 removed outlier: 3.703A pdb=" N SER E 110 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR E 121 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU E 108 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR E 123 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU E 106 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ARG E 125 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLN E 104 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR E 127 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASP E 102 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N LYS E 129 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLY E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 163 through 168 removed outlier: 7.082A pdb=" N SER E 163 " --> pdb=" O MET E 197 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET E 197 " --> pdb=" O SER E 163 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG E 165 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 110 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR E 121 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU E 108 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR E 123 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU E 106 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ARG E 125 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLN E 104 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR E 127 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASP E 102 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N LYS E 129 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLY E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.651A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N SER E 218 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASN E 269 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR E 276 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU E 252 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ARG E 278 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE E 250 " --> pdb=" O ARG E 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 143 through 145 removed outlier: 3.702A pdb=" N SER B 110 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR B 121 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU B 108 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR B 123 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU B 106 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ARG B 125 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLN B 104 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR B 127 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASP B 102 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N LYS B 129 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N GLY B 100 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 163 through 168 removed outlier: 7.084A pdb=" N SER B 163 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET B 197 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 165 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 110 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR B 121 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU B 108 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR B 123 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU B 106 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ARG B 125 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLN B 104 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR B 127 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASP B 102 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N LYS B 129 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N GLY B 100 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.650A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N SER B 218 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASN B 269 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR B 276 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU B 252 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ARG B 278 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE B 250 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.702A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR C 121 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU C 108 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR C 123 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU C 106 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ARG C 125 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLN C 104 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR C 127 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASP C 102 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N LYS C 129 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLY C 100 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 163 through 168 removed outlier: 7.082A pdb=" N SER C 163 " --> pdb=" O MET C 197 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET C 197 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 165 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR C 121 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU C 108 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR C 123 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU C 106 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ARG C 125 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLN C 104 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR C 127 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASP C 102 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N LYS C 129 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLY C 100 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.651A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N SER C 218 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASN C 269 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR C 276 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU C 252 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ARG C 278 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE C 250 " --> pdb=" O ARG C 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 143 through 145 removed outlier: 3.702A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR D 121 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU D 108 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR D 123 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU D 106 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ARG D 125 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLN D 104 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR D 127 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASP D 102 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N LYS D 129 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N GLY D 100 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 163 through 168 removed outlier: 7.084A pdb=" N SER D 163 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET D 197 " --> pdb=" O SER D 163 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG D 165 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR D 121 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU D 108 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR D 123 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU D 106 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ARG D 125 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLN D 104 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR D 127 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASP D 102 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N LYS D 129 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N GLY D 100 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.651A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N SER D 218 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASN D 269 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR D 276 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU D 252 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ARG D 278 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE D 250 " --> pdb=" O ARG D 278 " (cutoff:3.500A) 745 hydrogen bonds defined for protein. 2100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3975 1.35 - 1.47: 4080 1.47 - 1.60: 6415 1.60 - 1.72: 0 1.72 - 1.85: 140 Bond restraints: 14610 Sorted by residual: bond pdb=" C HIS C 169 " pdb=" N ASP C 170 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.42e-02 4.96e+03 5.79e+00 bond pdb=" C HIS E 169 " pdb=" N ASP E 170 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.42e-02 4.96e+03 5.73e+00 bond pdb=" C HIS B 169 " pdb=" N ASP B 170 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.42e-02 4.96e+03 5.71e+00 bond pdb=" C HIS A 169 " pdb=" N ASP A 170 " ideal model delta sigma weight residual 1.332 1.365 -0.034 1.42e-02 4.96e+03 5.69e+00 bond pdb=" C HIS D 169 " pdb=" N ASP D 170 " ideal model delta sigma weight residual 1.332 1.365 -0.034 1.42e-02 4.96e+03 5.62e+00 ... (remaining 14605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 17637 1.92 - 3.85: 1754 3.85 - 5.77: 299 5.77 - 7.70: 45 7.70 - 9.62: 10 Bond angle restraints: 19745 Sorted by residual: angle pdb=" N PHE E 290 " pdb=" CA PHE E 290 " pdb=" CB PHE E 290 " ideal model delta sigma weight residual 110.42 104.78 5.64 1.18e+00 7.18e-01 2.28e+01 angle pdb=" N PHE D 290 " pdb=" CA PHE D 290 " pdb=" CB PHE D 290 " ideal model delta sigma weight residual 110.42 104.81 5.61 1.18e+00 7.18e-01 2.26e+01 angle pdb=" N PHE A 290 " pdb=" CA PHE A 290 " pdb=" CB PHE A 290 " ideal model delta sigma weight residual 110.42 104.82 5.60 1.18e+00 7.18e-01 2.25e+01 angle pdb=" N PHE C 290 " pdb=" CA PHE C 290 " pdb=" CB PHE C 290 " ideal model delta sigma weight residual 110.42 104.84 5.58 1.18e+00 7.18e-01 2.24e+01 angle pdb=" N PHE B 290 " pdb=" CA PHE B 290 " pdb=" CB PHE B 290 " ideal model delta sigma weight residual 110.42 104.87 5.55 1.18e+00 7.18e-01 2.22e+01 ... (remaining 19740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8353 17.96 - 35.92: 403 35.92 - 53.88: 55 53.88 - 71.84: 25 71.84 - 89.80: 15 Dihedral angle restraints: 8851 sinusoidal: 3896 harmonic: 4955 Sorted by residual: dihedral pdb=" CA LEU C 108 " pdb=" C LEU C 108 " pdb=" N ASP C 109 " pdb=" CA ASP C 109 " ideal model delta harmonic sigma weight residual 180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LEU E 108 " pdb=" C LEU E 108 " pdb=" N ASP E 109 " pdb=" CA ASP E 109 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU A 108 " pdb=" C LEU A 108 " pdb=" N ASP A 109 " pdb=" CA ASP A 109 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 8848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 2074 0.125 - 0.249: 136 0.249 - 0.374: 5 0.374 - 0.499: 5 0.499 - 0.624: 15 Chirality restraints: 2235 Sorted by residual: 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 -1.78 -0.62 2.00e-01 2.50e+01 9.72e+00 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.67e+00 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 -1.78 -0.62 2.00e-01 2.50e+01 9.64e+00 ... (remaining 2232 not shown) Planarity restraints: 2390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.231 2.00e-02 2.50e+03 2.52e-01 7.91e+02 pdb=" CG ASN A 234 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.415 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " -0.290 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " -0.231 2.00e-02 2.50e+03 2.52e-01 7.91e+02 pdb=" CG ASN B 234 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " 0.415 2.00e-02 2.50e+03 pdb=" C1 NAG B 502 " -0.290 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " 0.231 2.00e-02 2.50e+03 2.51e-01 7.90e+02 pdb=" CG ASN C 234 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " -0.415 2.00e-02 2.50e+03 pdb=" C1 NAG C 503 " 0.290 2.00e-02 2.50e+03 ... (remaining 2387 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 41 2.61 - 3.19: 11176 3.19 - 3.76: 19375 3.76 - 4.33: 30857 4.33 - 4.90: 49339 Nonbonded interactions: 110788 Sorted by model distance: nonbonded pdb=" SG CYS C 198 " pdb=" SG CYS C 212 " model vdw 2.042 3.760 nonbonded pdb=" CG ASN C 140 " pdb=" O5 NAG C 502 " model vdw 2.388 2.616 nonbonded pdb=" CG ASN E 140 " pdb=" O5 NAG E 502 " model vdw 2.388 2.616 nonbonded pdb=" CG ASN A 140 " pdb=" O5 NAG A 501 " model vdw 2.389 2.616 nonbonded pdb=" CG ASN D 140 " pdb=" O5 NAG D 504 " model vdw 2.389 2.616 ... (remaining 110783 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 75 through 479 or resid 510)) selection = (chain 'B' and (resid 75 through 479 or resid 510)) selection = (chain 'C' and (resid 75 through 479 or resid 510)) selection = (chain 'D' and (resid 75 through 479 or resid 510)) selection = (chain 'E' and (resid 75 through 479 or resid 510)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 35.990 Find NCS groups from input model: 0.740 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: 0.000 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 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 : 0.011 0.205 14624 Z= 0.575 Angle : 1.471 32.778 19785 Z= 0.736 Chirality : 0.086 0.624 2235 Planarity : 0.014 0.115 2380 Dihedral : 12.014 89.802 5615 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.32 % Allowed : 1.62 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 1640 helix: 0.06 (0.20), residues: 510 sheet: 1.33 (0.24), residues: 400 loop : -0.31 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.009 TRP C 128 HIS 0.010 0.004 HIS E 254 PHE 0.046 0.007 PHE D 290 TYR 0.046 0.010 TYR C 272 ARG 0.027 0.004 ARG D 307 Details of bonding type rmsd link_NAG-ASN : bond 0.15129 ( 10) link_NAG-ASN : angle 19.48825 ( 30) hydrogen bonds : bond 0.19231 ( 670) hydrogen bonds : angle 6.49260 ( 2100) SS BOND : bond 0.01070 ( 4) SS BOND : angle 1.88179 ( 10) covalent geometry : bond 0.00990 (14610) covalent geometry : angle 1.26118 (19745) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 282 time to evaluate : 1.542 Fit side-chains REVERT: A 174 ASP cc_start: 0.8410 (m-30) cc_final: 0.8144 (m-30) REVERT: A 345 ASP cc_start: 0.8732 (m-30) cc_final: 0.8529 (m-30) REVERT: E 88 MET cc_start: 0.7356 (ptp) cc_final: 0.7138 (ptt) REVERT: E 345 ASP cc_start: 0.8700 (m-30) cc_final: 0.8251 (m-30) REVERT: B 116 MET cc_start: 0.9152 (mtm) cc_final: 0.8884 (mtm) REVERT: B 345 ASP cc_start: 0.8739 (m-30) cc_final: 0.8341 (m-30) REVERT: C 88 MET cc_start: 0.7493 (ptp) cc_final: 0.7181 (ptt) REVERT: C 116 MET cc_start: 0.9058 (mtm) cc_final: 0.8810 (mtm) REVERT: C 178 LEU cc_start: 0.8872 (mt) cc_final: 0.8663 (tp) REVERT: C 225 ASP cc_start: 0.8094 (m-30) cc_final: 0.7889 (m-30) REVERT: C 345 ASP cc_start: 0.8627 (m-30) cc_final: 0.8418 (m-30) REVERT: D 88 MET cc_start: 0.7520 (ptp) cc_final: 0.7276 (ptt) outliers start: 5 outliers final: 1 residues processed: 282 average time/residue: 1.4710 time to fit residues: 447.8482 Evaluate side-chains 202 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 243 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0170 chunk 125 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 ASN D 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.170050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.142946 restraints weight = 13918.824| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.23 r_work: 0.3556 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14624 Z= 0.163 Angle : 0.760 23.697 19785 Z= 0.367 Chirality : 0.050 0.529 2235 Planarity : 0.006 0.054 2380 Dihedral : 7.531 76.127 2427 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.43 % Allowed : 7.21 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.20), residues: 1640 helix: 1.84 (0.23), residues: 535 sheet: 1.04 (0.23), residues: 490 loop : 0.30 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 349 HIS 0.004 0.001 HIS D 254 PHE 0.027 0.002 PHE B 290 TYR 0.017 0.002 TYR C 272 ARG 0.002 0.000 ARG A 165 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 10) link_NAG-ASN : angle 11.39994 ( 30) hydrogen bonds : bond 0.07260 ( 670) hydrogen bonds : angle 4.53991 ( 2100) SS BOND : bond 0.00467 ( 4) SS BOND : angle 0.94526 ( 10) covalent geometry : bond 0.00275 (14610) covalent geometry : angle 0.61746 (19745) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 1.742 Fit side-chains REVERT: A 134 SER cc_start: 0.8249 (p) cc_final: 0.7864 (t) REVERT: A 345 ASP cc_start: 0.8383 (m-30) cc_final: 0.7946 (m-30) REVERT: E 345 ASP cc_start: 0.8248 (m-30) cc_final: 0.7930 (m-30) REVERT: E 373 GLU cc_start: 0.6276 (mt-10) cc_final: 0.5937 (mp0) REVERT: B 134 SER cc_start: 0.8356 (p) cc_final: 0.7865 (t) REVERT: B 179 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7684 (ttm170) REVERT: B 295 MET cc_start: 0.8859 (mmp) cc_final: 0.8610 (mmm) REVERT: B 345 ASP cc_start: 0.8376 (m-30) cc_final: 0.7853 (m-30) REVERT: B 373 GLU cc_start: 0.5913 (mt-10) cc_final: 0.5676 (mp0) REVERT: C 116 MET cc_start: 0.8757 (mtm) cc_final: 0.8472 (mtm) REVERT: C 134 SER cc_start: 0.8332 (p) cc_final: 0.7924 (t) REVERT: C 225 ASP cc_start: 0.7848 (m-30) cc_final: 0.7564 (m-30) REVERT: C 345 ASP cc_start: 0.8179 (m-30) cc_final: 0.7748 (m-30) REVERT: C 373 GLU cc_start: 0.6031 (mt-10) cc_final: 0.5784 (mp0) REVERT: D 179 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7674 (ttm170) REVERT: D 241 GLU cc_start: 0.7044 (tt0) cc_final: 0.6762 (mp0) REVERT: D 373 GLU cc_start: 0.6062 (mt-10) cc_final: 0.5735 (mp0) outliers start: 22 outliers final: 9 residues processed: 241 average time/residue: 1.4517 time to fit residues: 378.8829 Evaluate side-chains 216 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN E 247 GLN B 247 GLN C 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.164776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137740 restraints weight = 13716.962| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.19 r_work: 0.3059 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14624 Z= 0.210 Angle : 0.795 21.863 19785 Z= 0.401 Chirality : 0.052 0.519 2235 Planarity : 0.006 0.056 2380 Dihedral : 7.272 74.514 2425 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.08 % Allowed : 8.18 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.20), residues: 1640 helix: 2.16 (0.22), residues: 530 sheet: 1.05 (0.24), residues: 470 loop : 0.04 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 230 HIS 0.006 0.002 HIS C 254 PHE 0.026 0.002 PHE B 290 TYR 0.014 0.002 TYR A 362 ARG 0.003 0.001 ARG D 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01394 ( 10) link_NAG-ASN : angle 10.67506 ( 30) hydrogen bonds : bond 0.09615 ( 670) hydrogen bonds : angle 4.66418 ( 2100) SS BOND : bond 0.00903 ( 4) SS BOND : angle 1.52292 ( 10) covalent geometry : bond 0.00372 (14610) covalent geometry : angle 0.67733 (19745) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 1.597 Fit side-chains REVERT: A 88 MET cc_start: 0.7882 (ptp) cc_final: 0.7427 (ptt) REVERT: A 134 SER cc_start: 0.8203 (p) cc_final: 0.7804 (t) REVERT: A 227 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7534 (tmt) REVERT: A 241 GLU cc_start: 0.7506 (tt0) cc_final: 0.7236 (mp0) REVERT: E 88 MET cc_start: 0.7871 (ptp) cc_final: 0.7412 (ptt) REVERT: E 179 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7610 (ttm170) REVERT: E 241 GLU cc_start: 0.6801 (mp0) cc_final: 0.6556 (mp0) REVERT: E 345 ASP cc_start: 0.8568 (m-30) cc_final: 0.8163 (m-30) REVERT: B 134 SER cc_start: 0.8275 (p) cc_final: 0.7814 (t) REVERT: B 179 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7617 (ttm170) REVERT: B 345 ASP cc_start: 0.8588 (m-30) cc_final: 0.8121 (m-30) REVERT: C 134 SER cc_start: 0.8361 (p) cc_final: 0.7951 (t) REVERT: C 179 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7769 (ttm170) REVERT: C 373 GLU cc_start: 0.6116 (mt-10) cc_final: 0.5709 (mp0) REVERT: C 457 LYS cc_start: 0.8334 (mtmt) cc_final: 0.7935 (mmtp) REVERT: D 179 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7712 (ttm170) REVERT: D 241 GLU cc_start: 0.7484 (tt0) cc_final: 0.7093 (mp0) outliers start: 32 outliers final: 16 residues processed: 235 average time/residue: 1.4698 time to fit residues: 373.0246 Evaluate side-chains 228 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 344 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.158362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128679 restraints weight = 13839.466| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.28 r_work: 0.3072 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14624 Z= 0.180 Angle : 0.722 20.877 19785 Z= 0.363 Chirality : 0.049 0.489 2235 Planarity : 0.005 0.052 2380 Dihedral : 7.062 68.784 2425 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.14 % Allowed : 10.00 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.20), residues: 1640 helix: 2.42 (0.22), residues: 530 sheet: 1.26 (0.24), residues: 440 loop : 0.01 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 349 HIS 0.006 0.002 HIS C 254 PHE 0.022 0.002 PHE B 290 TYR 0.013 0.002 TYR C 272 ARG 0.002 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01591 ( 10) link_NAG-ASN : angle 9.97083 ( 30) hydrogen bonds : bond 0.08335 ( 670) hydrogen bonds : angle 4.42730 ( 2100) SS BOND : bond 0.00744 ( 4) SS BOND : angle 1.22801 ( 10) covalent geometry : bond 0.00310 (14610) covalent geometry : angle 0.60890 (19745) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 1.524 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.7892 (ptp) cc_final: 0.7441 (ptt) REVERT: A 134 SER cc_start: 0.8122 (p) cc_final: 0.7731 (t) REVERT: A 181 GLN cc_start: 0.8465 (mm110) cc_final: 0.7900 (mt0) REVERT: A 227 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7523 (tmt) REVERT: A 345 ASP cc_start: 0.8545 (m-30) cc_final: 0.8063 (m-30) REVERT: A 457 LYS cc_start: 0.8346 (mmtp) cc_final: 0.7921 (mmtt) REVERT: E 88 MET cc_start: 0.7944 (ptp) cc_final: 0.7496 (ptt) REVERT: E 179 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7567 (ttm170) REVERT: E 227 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7386 (tmt) REVERT: E 238 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8212 (mptp) REVERT: E 345 ASP cc_start: 0.8492 (m-30) cc_final: 0.8081 (m-30) REVERT: B 134 SER cc_start: 0.8104 (p) cc_final: 0.7689 (t) REVERT: B 345 ASP cc_start: 0.8541 (m-30) cc_final: 0.8094 (m-30) REVERT: C 134 SER cc_start: 0.8275 (p) cc_final: 0.7873 (t) REVERT: C 179 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7819 (ttm170) REVERT: C 373 GLU cc_start: 0.6035 (mt-10) cc_final: 0.5632 (mp0) REVERT: C 457 LYS cc_start: 0.8301 (mtmt) cc_final: 0.7838 (mmtt) REVERT: D 241 GLU cc_start: 0.7530 (tt0) cc_final: 0.7090 (mp0) REVERT: D 457 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7840 (mmtt) outliers start: 33 outliers final: 18 residues processed: 236 average time/residue: 1.3835 time to fit residues: 354.2857 Evaluate side-chains 232 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 457 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 17 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 139 optimal weight: 0.4980 chunk 36 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.160640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132776 restraints weight = 13978.902| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.23 r_work: 0.3053 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14624 Z= 0.204 Angle : 0.759 20.808 19785 Z= 0.386 Chirality : 0.050 0.479 2235 Planarity : 0.006 0.052 2380 Dihedral : 7.357 63.851 2425 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.40 % Allowed : 11.10 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.20), residues: 1640 helix: 2.41 (0.22), residues: 530 sheet: 1.22 (0.24), residues: 440 loop : -0.10 (0.20), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 349 HIS 0.006 0.002 HIS C 254 PHE 0.020 0.002 PHE B 356 TYR 0.014 0.002 TYR A 362 ARG 0.003 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01657 ( 10) link_NAG-ASN : angle 9.87820 ( 30) hydrogen bonds : bond 0.09346 ( 670) hydrogen bonds : angle 4.53519 ( 2100) SS BOND : bond 0.00981 ( 4) SS BOND : angle 1.59178 ( 10) covalent geometry : bond 0.00363 (14610) covalent geometry : angle 0.65364 (19745) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 1.734 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.8026 (ptp) cc_final: 0.7591 (ptt) REVERT: A 134 SER cc_start: 0.8172 (p) cc_final: 0.7766 (t) REVERT: A 181 GLN cc_start: 0.8538 (mm110) cc_final: 0.7985 (mt0) REVERT: A 227 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7670 (tmt) REVERT: A 457 LYS cc_start: 0.8402 (mmtp) cc_final: 0.7987 (mmtt) REVERT: E 88 MET cc_start: 0.7985 (ptp) cc_final: 0.7561 (ptt) REVERT: E 179 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7613 (ttm170) REVERT: E 227 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7437 (tmt) REVERT: E 345 ASP cc_start: 0.8604 (m-30) cc_final: 0.7985 (m-30) REVERT: B 134 SER cc_start: 0.8201 (p) cc_final: 0.7767 (t) REVERT: B 179 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7593 (ttm170) REVERT: B 258 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8020 (ttmt) REVERT: B 345 ASP cc_start: 0.8625 (m-30) cc_final: 0.8032 (m-30) REVERT: C 88 MET cc_start: 0.7936 (ptp) cc_final: 0.7642 (ptt) REVERT: C 134 SER cc_start: 0.8309 (p) cc_final: 0.7894 (t) REVERT: C 179 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7827 (ttm170) REVERT: C 238 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8271 (mptp) REVERT: C 324 MET cc_start: 0.9075 (tpt) cc_final: 0.8873 (tpp) REVERT: C 457 LYS cc_start: 0.8349 (mtmt) cc_final: 0.7921 (mmtt) REVERT: D 88 MET cc_start: 0.7930 (ptp) cc_final: 0.7654 (ptt) REVERT: D 179 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7717 (ttm170) REVERT: D 238 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8318 (mptp) REVERT: D 241 GLU cc_start: 0.7629 (tt0) cc_final: 0.7227 (mp0) REVERT: D 457 LYS cc_start: 0.8277 (tptt) cc_final: 0.7900 (mmtt) outliers start: 37 outliers final: 21 residues processed: 233 average time/residue: 1.5644 time to fit residues: 393.5760 Evaluate side-chains 230 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 344 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 105 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.159957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.132154 restraints weight = 13998.684| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.23 r_work: 0.3059 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14624 Z= 0.210 Angle : 0.767 20.634 19785 Z= 0.393 Chirality : 0.050 0.468 2235 Planarity : 0.006 0.053 2380 Dihedral : 7.387 53.629 2425 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.66 % Allowed : 11.75 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.20), residues: 1640 helix: 2.41 (0.22), residues: 530 sheet: 1.23 (0.24), residues: 440 loop : -0.12 (0.20), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 349 HIS 0.006 0.002 HIS C 254 PHE 0.020 0.002 PHE B 356 TYR 0.014 0.002 TYR A 362 ARG 0.003 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01577 ( 10) link_NAG-ASN : angle 9.70715 ( 30) hydrogen bonds : bond 0.09553 ( 670) hydrogen bonds : angle 4.52550 ( 2100) SS BOND : bond 0.01052 ( 4) SS BOND : angle 1.60606 ( 10) covalent geometry : bond 0.00381 (14610) covalent geometry : angle 0.66655 (19745) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.7989 (ptp) cc_final: 0.7624 (ptt) REVERT: A 134 SER cc_start: 0.8200 (p) cc_final: 0.7783 (t) REVERT: A 181 GLN cc_start: 0.8508 (mm110) cc_final: 0.7973 (mt0) REVERT: A 227 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7639 (tmt) REVERT: A 238 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8353 (mptp) REVERT: A 457 LYS cc_start: 0.8385 (mmtp) cc_final: 0.7958 (mmtt) REVERT: E 88 MET cc_start: 0.7998 (ptp) cc_final: 0.7588 (ptt) REVERT: E 179 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7626 (ttm170) REVERT: E 238 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8309 (mptp) REVERT: E 345 ASP cc_start: 0.8592 (m-30) cc_final: 0.7855 (m-30) REVERT: B 134 SER cc_start: 0.8247 (p) cc_final: 0.7793 (t) REVERT: B 179 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7606 (ttm170) REVERT: B 258 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8000 (ttmt) REVERT: C 88 MET cc_start: 0.7973 (ptp) cc_final: 0.7701 (ptt) REVERT: C 179 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7905 (ttm170) REVERT: C 238 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8334 (mptp) REVERT: C 457 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7952 (mmtt) REVERT: D 179 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7754 (ttm170) REVERT: D 238 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8307 (mptp) REVERT: D 241 GLU cc_start: 0.7650 (tt0) cc_final: 0.7229 (mp0) REVERT: D 457 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7905 (mmtt) outliers start: 41 outliers final: 21 residues processed: 233 average time/residue: 1.5367 time to fit residues: 386.3815 Evaluate side-chains 222 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 457 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.159128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.131374 restraints weight = 13993.676| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.23 r_work: 0.3049 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14624 Z= 0.220 Angle : 0.782 20.621 19785 Z= 0.402 Chirality : 0.050 0.469 2235 Planarity : 0.006 0.052 2380 Dihedral : 7.380 57.174 2425 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.34 % Allowed : 12.27 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.20), residues: 1640 helix: 2.39 (0.22), residues: 530 sheet: 1.21 (0.24), residues: 440 loop : -0.17 (0.20), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 349 HIS 0.006 0.002 HIS E 254 PHE 0.021 0.002 PHE B 356 TYR 0.015 0.002 TYR A 362 ARG 0.003 0.000 ARG D 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01620 ( 10) link_NAG-ASN : angle 9.71882 ( 30) hydrogen bonds : bond 0.09886 ( 670) hydrogen bonds : angle 4.55497 ( 2100) SS BOND : bond 0.01055 ( 4) SS BOND : angle 1.66730 ( 10) covalent geometry : bond 0.00403 (14610) covalent geometry : angle 0.68421 (19745) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7986 (ptp) cc_final: 0.7634 (ptt) REVERT: A 134 SER cc_start: 0.8219 (p) cc_final: 0.7799 (t) REVERT: A 181 GLN cc_start: 0.8524 (mm110) cc_final: 0.7978 (mt0) REVERT: A 227 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7622 (tmt) REVERT: A 238 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8385 (mptp) REVERT: A 457 LYS cc_start: 0.8390 (mmtp) cc_final: 0.7965 (mmtt) REVERT: E 88 MET cc_start: 0.8017 (ptp) cc_final: 0.7603 (ptt) REVERT: E 179 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7628 (ttm170) REVERT: E 238 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8316 (mptp) REVERT: B 134 SER cc_start: 0.8280 (p) cc_final: 0.7816 (t) REVERT: B 179 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7613 (ttm170) REVERT: C 88 MET cc_start: 0.7974 (ptp) cc_final: 0.7714 (ptt) REVERT: C 134 SER cc_start: 0.8472 (p) cc_final: 0.8013 (t) REVERT: C 179 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7923 (ttm170) REVERT: C 238 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8357 (mptp) REVERT: C 457 LYS cc_start: 0.8387 (mtmt) cc_final: 0.7951 (mmtt) REVERT: D 88 MET cc_start: 0.7960 (ptp) cc_final: 0.7667 (ptt) REVERT: D 179 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7761 (ttm170) REVERT: D 238 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8310 (mptp) REVERT: D 241 GLU cc_start: 0.7660 (tt0) cc_final: 0.7210 (mp0) REVERT: D 457 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7915 (mmtt) outliers start: 36 outliers final: 20 residues processed: 224 average time/residue: 1.4504 time to fit residues: 351.8442 Evaluate side-chains 214 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 457 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.159790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.132062 restraints weight = 13977.531| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.23 r_work: 0.3046 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14624 Z= 0.211 Angle : 0.769 20.545 19785 Z= 0.394 Chirality : 0.050 0.491 2235 Planarity : 0.006 0.051 2380 Dihedral : 7.259 58.762 2425 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.53 % Allowed : 12.21 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.20), residues: 1640 helix: 2.42 (0.22), residues: 530 sheet: 1.21 (0.24), residues: 440 loop : -0.18 (0.20), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 349 HIS 0.006 0.002 HIS E 254 PHE 0.020 0.002 PHE B 356 TYR 0.015 0.002 TYR A 362 ARG 0.003 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01661 ( 10) link_NAG-ASN : angle 9.70988 ( 30) hydrogen bonds : bond 0.09537 ( 670) hydrogen bonds : angle 4.51447 ( 2100) SS BOND : bond 0.01089 ( 4) SS BOND : angle 1.67639 ( 10) covalent geometry : bond 0.00384 (14610) covalent geometry : angle 0.66874 (19745) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 1.625 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.8005 (ptp) cc_final: 0.7657 (OUTLIER) REVERT: A 134 SER cc_start: 0.8233 (p) cc_final: 0.7824 (t) REVERT: A 181 GLN cc_start: 0.8524 (mm110) cc_final: 0.7979 (mt0) REVERT: A 225 ASP cc_start: 0.8079 (m-30) cc_final: 0.7805 (m-30) REVERT: A 227 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7615 (tmt) REVERT: E 88 MET cc_start: 0.8032 (ptp) cc_final: 0.7619 (ptt) REVERT: E 179 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7636 (ttm170) REVERT: E 238 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8316 (mptp) REVERT: E 345 ASP cc_start: 0.8600 (m-30) cc_final: 0.7856 (m-30) REVERT: B 134 SER cc_start: 0.8287 (p) cc_final: 0.7824 (t) REVERT: B 179 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7611 (ttm170) REVERT: C 88 MET cc_start: 0.8016 (ptp) cc_final: 0.7744 (ptt) REVERT: C 134 SER cc_start: 0.8453 (p) cc_final: 0.7991 (t) REVERT: C 179 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7881 (ttm170) REVERT: C 238 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8334 (mptp) REVERT: C 457 LYS cc_start: 0.8363 (mtmt) cc_final: 0.7922 (mmtt) REVERT: D 88 MET cc_start: 0.8021 (ptp) cc_final: 0.7722 (ptt) REVERT: D 179 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7742 (ttm170) REVERT: D 238 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8297 (mptp) REVERT: D 241 GLU cc_start: 0.7646 (tt0) cc_final: 0.7216 (mp0) REVERT: D 457 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7884 (mmtt) outliers start: 39 outliers final: 24 residues processed: 219 average time/residue: 1.3772 time to fit residues: 327.8063 Evaluate side-chains 216 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 457 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 139 optimal weight: 0.4980 chunk 26 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN C 254 HIS D 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.167600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140989 restraints weight = 14129.059| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.22 r_work: 0.3509 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14624 Z= 0.138 Angle : 0.637 20.262 19785 Z= 0.314 Chirality : 0.046 0.509 2235 Planarity : 0.005 0.049 2380 Dihedral : 6.151 55.109 2425 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.01 % Allowed : 13.05 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.20), residues: 1640 helix: 2.73 (0.22), residues: 535 sheet: 0.93 (0.24), residues: 465 loop : 0.10 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 349 HIS 0.005 0.001 HIS B 254 PHE 0.016 0.001 PHE B 290 TYR 0.015 0.001 TYR D 340 ARG 0.002 0.000 ARG E 191 Details of bonding type rmsd link_NAG-ASN : bond 0.01745 ( 10) link_NAG-ASN : angle 9.55870 ( 30) hydrogen bonds : bond 0.06428 ( 670) hydrogen bonds : angle 4.17468 ( 2100) SS BOND : bond 0.00465 ( 4) SS BOND : angle 0.79015 ( 10) covalent geometry : bond 0.00225 (14610) covalent geometry : angle 0.51709 (19745) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7864 (ptp) cc_final: 0.7530 (OUTLIER) REVERT: A 227 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7513 (tmt) REVERT: A 257 THR cc_start: 0.9106 (p) cc_final: 0.8885 (p) REVERT: A 345 ASP cc_start: 0.8230 (m-30) cc_final: 0.7980 (m-30) REVERT: E 88 MET cc_start: 0.7998 (ptp) cc_final: 0.7636 (ptt) REVERT: E 179 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7562 (ttm170) REVERT: E 345 ASP cc_start: 0.8233 (m-30) cc_final: 0.7981 (m-30) REVERT: B 345 ASP cc_start: 0.8266 (m-30) cc_final: 0.8049 (m-30) REVERT: C 88 MET cc_start: 0.7976 (ptp) cc_final: 0.7690 (ptt) REVERT: C 134 SER cc_start: 0.8300 (p) cc_final: 0.7888 (t) REVERT: C 179 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7691 (ttm170) REVERT: C 345 ASP cc_start: 0.8254 (m-30) cc_final: 0.7468 (m-30) REVERT: C 457 LYS cc_start: 0.8246 (mtmt) cc_final: 0.7876 (mmtm) REVERT: D 88 MET cc_start: 0.7731 (ptp) cc_final: 0.7406 (ptt) REVERT: D 179 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7687 (ttm170) REVERT: D 241 GLU cc_start: 0.7573 (tt0) cc_final: 0.7322 (mp0) REVERT: D 345 ASP cc_start: 0.8282 (m-30) cc_final: 0.7641 (m-30) REVERT: D 457 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7842 (mmtt) outliers start: 31 outliers final: 14 residues processed: 216 average time/residue: 1.4244 time to fit residues: 334.5576 Evaluate side-chains 206 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 457 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 111 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 46 optimal weight: 0.0020 chunk 110 optimal weight: 5.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133618 restraints weight = 13497.577| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.21 r_work: 0.3021 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14624 Z= 0.260 Angle : 0.857 21.014 19785 Z= 0.444 Chirality : 0.053 0.514 2235 Planarity : 0.006 0.056 2380 Dihedral : 7.538 56.956 2425 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.30 % Allowed : 14.03 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.20), residues: 1640 helix: 2.38 (0.22), residues: 530 sheet: 1.27 (0.24), residues: 440 loop : -0.24 (0.20), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 230 HIS 0.007 0.002 HIS E 254 PHE 0.021 0.003 PHE B 356 TYR 0.016 0.003 TYR A 362 ARG 0.005 0.001 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01662 ( 10) link_NAG-ASN : angle 9.80168 ( 30) hydrogen bonds : bond 0.10829 ( 670) hydrogen bonds : angle 4.60717 ( 2100) SS BOND : bond 0.01717 ( 4) SS BOND : angle 3.53018 ( 10) covalent geometry : bond 0.00513 (14610) covalent geometry : angle 0.76355 (19745) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7941 (ptp) cc_final: 0.7580 (OUTLIER) REVERT: A 134 SER cc_start: 0.8228 (p) cc_final: 0.7820 (t) REVERT: A 225 ASP cc_start: 0.8127 (m-30) cc_final: 0.7872 (m-30) REVERT: A 227 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7618 (tmt) REVERT: E 88 MET cc_start: 0.8019 (ptp) cc_final: 0.7592 (ptt) REVERT: E 179 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7653 (ttm170) REVERT: B 134 SER cc_start: 0.8286 (p) cc_final: 0.7834 (t) REVERT: B 241 GLU cc_start: 0.7045 (mp0) cc_final: 0.6735 (mp0) REVERT: B 457 LYS cc_start: 0.8252 (tptt) cc_final: 0.7899 (mmtt) REVERT: C 88 MET cc_start: 0.8010 (ptp) cc_final: 0.7732 (ptt) REVERT: C 134 SER cc_start: 0.8463 (p) cc_final: 0.8006 (t) REVERT: C 179 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7914 (ttm170) REVERT: C 457 LYS cc_start: 0.8392 (mtmt) cc_final: 0.7964 (mmtt) REVERT: D 88 MET cc_start: 0.7968 (ptp) cc_final: 0.7671 (ptt) REVERT: D 179 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7758 (ttm170) REVERT: D 241 GLU cc_start: 0.7639 (tt0) cc_final: 0.7268 (mp0) REVERT: D 457 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7906 (mmtt) outliers start: 20 outliers final: 11 residues processed: 213 average time/residue: 1.4298 time to fit residues: 330.2658 Evaluate side-chains 198 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 457 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 112 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.164657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137514 restraints weight = 13923.091| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.23 r_work: 0.3099 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14624 Z= 0.183 Angle : 0.727 20.699 19785 Z= 0.368 Chirality : 0.048 0.531 2235 Planarity : 0.005 0.050 2380 Dihedral : 6.934 58.787 2425 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.10 % Allowed : 14.42 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.20), residues: 1640 helix: 2.52 (0.22), residues: 530 sheet: 1.17 (0.24), residues: 440 loop : -0.14 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 349 HIS 0.005 0.001 HIS E 254 PHE 0.018 0.002 PHE B 356 TYR 0.014 0.002 TYR A 362 ARG 0.002 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01704 ( 10) link_NAG-ASN : angle 9.68602 ( 30) hydrogen bonds : bond 0.08597 ( 670) hydrogen bonds : angle 4.45467 ( 2100) SS BOND : bond 0.01503 ( 4) SS BOND : angle 0.90979 ( 10) covalent geometry : bond 0.00313 (14610) covalent geometry : angle 0.62203 (19745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11195.72 seconds wall clock time: 193 minutes 3.18 seconds (11583.18 seconds total)