Starting phenix.real_space_refine on Thu Jun 12 19:49:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rh4_19167/06_2025/8rh4_19167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rh4_19167/06_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_19167/06_2025/8rh4_19167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rh4_19167/06_2025/8rh4_19167.map" model { file = "/net/cci-nas-00/data/ceres_data/8rh4_19167/06_2025/8rh4_19167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rh4_19167/06_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-5710/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: 10.48, per 1000 atoms: 0.73 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: 3.44 Conformation dependent library (CDL) restraints added in 1.8 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: 1.62 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: 4.09 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: 5.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.520 Find NCS groups from input model: 0.810 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.520 ------------------------------------------------------------------------------- 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 : 1.717 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: 1.5505 time to fit residues: 473.9859 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 : 1.702 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.142946 restraints weight = 13918.826| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.23 r_work: 0.3560 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 1.524 Fit side-chains REVERT: A 134 SER cc_start: 0.8244 (p) cc_final: 0.7859 (t) REVERT: A 345 ASP cc_start: 0.8364 (m-30) cc_final: 0.7924 (m-30) REVERT: E 345 ASP cc_start: 0.8233 (m-30) cc_final: 0.7912 (m-30) REVERT: E 373 GLU cc_start: 0.6256 (mt-10) cc_final: 0.5916 (mp0) REVERT: B 134 SER cc_start: 0.8346 (p) cc_final: 0.7856 (t) REVERT: B 179 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7667 (ttm170) REVERT: B 295 MET cc_start: 0.8852 (mmp) cc_final: 0.8599 (mmm) REVERT: B 345 ASP cc_start: 0.8355 (m-30) cc_final: 0.7827 (m-30) REVERT: B 373 GLU cc_start: 0.5898 (mt-10) cc_final: 0.5659 (mp0) REVERT: C 116 MET cc_start: 0.8747 (mtm) cc_final: 0.8462 (mtm) REVERT: C 134 SER cc_start: 0.8325 (p) cc_final: 0.7918 (t) REVERT: C 225 ASP cc_start: 0.7835 (m-30) cc_final: 0.7547 (m-30) REVERT: C 345 ASP cc_start: 0.8163 (m-30) cc_final: 0.7728 (m-30) REVERT: C 373 GLU cc_start: 0.6015 (mt-10) cc_final: 0.5766 (mp0) REVERT: D 179 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7654 (ttm170) REVERT: D 241 GLU cc_start: 0.7025 (tt0) cc_final: 0.6753 (mp0) REVERT: D 373 GLU cc_start: 0.6058 (mt-10) cc_final: 0.5725 (mp0) outliers start: 22 outliers final: 9 residues processed: 241 average time/residue: 1.5228 time to fit residues: 396.3254 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 : 1.705 ------------------------------------------------------------------------------- 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: 6.9990 chunk 2 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 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 = 0.3855 r_free = 0.3855 target = 0.164840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137766 restraints weight = 13716.447| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.19 r_work: 0.3060 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2934 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= 0.209 Angle : 0.794 21.790 19785 Z= 0.400 Chirality : 0.052 0.517 2235 Planarity : 0.006 0.056 2380 Dihedral : 7.268 74.483 2425 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.14 % Allowed : 8.12 % 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: 2.15 (0.22), residues: 530 sheet: 1.05 (0.24), residues: 470 loop : 0.05 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 128 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 0.01318 ( 10) link_NAG-ASN : angle 10.66477 ( 30) hydrogen bonds : bond 0.09550 ( 670) hydrogen bonds : angle 4.65919 ( 2100) SS BOND : bond 0.00886 ( 4) SS BOND : angle 1.47410 ( 10) covalent geometry : bond 0.00369 (14610) covalent geometry : angle 0.67650 (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 247 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 1.473 Fit side-chains REVERT: A 88 MET cc_start: 0.7878 (ptp) cc_final: 0.7420 (ptt) REVERT: A 134 SER cc_start: 0.8203 (p) cc_final: 0.7802 (t) REVERT: A 227 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7533 (tmt) REVERT: A 241 GLU cc_start: 0.7503 (tt0) cc_final: 0.7233 (mp0) REVERT: E 88 MET cc_start: 0.7868 (ptp) cc_final: 0.7408 (ptt) REVERT: E 179 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7606 (ttm170) REVERT: E 241 GLU cc_start: 0.6786 (mp0) cc_final: 0.6541 (mp0) REVERT: E 345 ASP cc_start: 0.8567 (m-30) cc_final: 0.8158 (m-30) REVERT: B 134 SER cc_start: 0.8276 (p) cc_final: 0.7812 (t) REVERT: B 179 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7618 (ttm170) REVERT: B 345 ASP cc_start: 0.8595 (m-30) cc_final: 0.8133 (m-30) REVERT: C 134 SER cc_start: 0.8350 (p) cc_final: 0.7937 (t) REVERT: C 179 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7767 (ttm170) REVERT: C 373 GLU cc_start: 0.6113 (mt-10) cc_final: 0.5705 (mp0) REVERT: C 457 LYS cc_start: 0.8336 (mtmt) cc_final: 0.7935 (mmtp) REVERT: D 179 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7713 (ttm170) REVERT: D 241 GLU cc_start: 0.7483 (tt0) cc_final: 0.7094 (mp0) outliers start: 33 outliers final: 14 residues processed: 236 average time/residue: 1.4925 time to fit residues: 380.4763 Evaluate side-chains 226 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 179 ARG 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: 3.9990 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 99 optimal weight: 0.0070 chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.158571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128914 restraints weight = 13846.169| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.28 r_work: 0.3073 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3205 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= 0.177 Angle : 0.719 20.930 19785 Z= 0.361 Chirality : 0.049 0.496 2235 Planarity : 0.005 0.052 2380 Dihedral : 7.037 68.608 2425 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.77 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: 1.68 (0.20), residues: 1640 helix: 2.43 (0.22), residues: 530 sheet: 1.01 (0.24), residues: 470 loop : 0.12 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 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 D 340 ARG 0.002 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01421 ( 10) link_NAG-ASN : angle 9.95411 ( 30) hydrogen bonds : bond 0.08276 ( 670) hydrogen bonds : angle 4.41863 ( 2100) SS BOND : bond 0.00719 ( 4) SS BOND : angle 1.22151 ( 10) covalent geometry : bond 0.00306 (14610) covalent geometry : angle 0.60584 (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 247 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.7892 (ptp) cc_final: 0.7436 (ptt) REVERT: A 134 SER cc_start: 0.8114 (p) cc_final: 0.7726 (t) REVERT: A 181 GLN cc_start: 0.8488 (mm110) cc_final: 0.7919 (mt0) REVERT: A 227 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7527 (tmt) REVERT: A 345 ASP cc_start: 0.8530 (m-30) cc_final: 0.8072 (m-30) REVERT: A 457 LYS cc_start: 0.8342 (mmtp) cc_final: 0.7917 (mmtt) REVERT: E 88 MET cc_start: 0.7941 (ptp) cc_final: 0.7493 (ptt) REVERT: E 179 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7540 (ttm170) REVERT: E 227 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7390 (tmt) REVERT: E 238 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8230 (mptp) REVERT: E 345 ASP cc_start: 0.8487 (m-30) cc_final: 0.8098 (m-30) REVERT: B 134 SER cc_start: 0.8093 (p) cc_final: 0.7681 (t) REVERT: B 238 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8388 (mptp) REVERT: B 345 ASP cc_start: 0.8537 (m-30) cc_final: 0.8068 (m-30) REVERT: C 134 SER cc_start: 0.8276 (p) cc_final: 0.7877 (t) REVERT: C 179 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7813 (ttm170) REVERT: C 373 GLU cc_start: 0.6040 (mt-10) cc_final: 0.5634 (mp0) REVERT: C 457 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7836 (mmtt) REVERT: D 241 GLU cc_start: 0.7535 (tt0) cc_final: 0.7076 (mp0) REVERT: D 457 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7838 (mmtt) outliers start: 33 outliers final: 19 residues processed: 235 average time/residue: 1.4030 time to fit residues: 358.2122 Evaluate side-chains 235 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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 235 ASP 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 238 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 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: 0.5980 chunk 65 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.163567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136314 restraints weight = 13770.066| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.22 r_work: 0.3046 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14624 Z= 0.210 Angle : 0.770 20.864 19785 Z= 0.393 Chirality : 0.050 0.475 2235 Planarity : 0.006 0.053 2380 Dihedral : 7.421 64.028 2425 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.40 % Allowed : 10.84 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.20), residues: 1640 helix: 2.39 (0.22), residues: 530 sheet: 1.22 (0.24), residues: 440 loop : -0.11 (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 0.015 0.002 TYR A 362 ARG 0.003 0.000 ARG D 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01513 ( 10) link_NAG-ASN : angle 9.89417 ( 30) hydrogen bonds : bond 0.09536 ( 670) hydrogen bonds : angle 4.55101 ( 2100) SS BOND : bond 0.01126 ( 4) SS BOND : angle 1.63538 ( 10) covalent geometry : bond 0.00379 (14610) covalent geometry : angle 0.66581 (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 242 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 1.485 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.8020 (ptp) cc_final: 0.7587 (ptt) REVERT: A 134 SER cc_start: 0.8177 (p) cc_final: 0.7766 (t) REVERT: A 181 GLN cc_start: 0.8538 (mm110) cc_final: 0.7979 (mt0) REVERT: A 227 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7656 (tmt) REVERT: A 457 LYS cc_start: 0.8404 (mmtp) cc_final: 0.7987 (mmtt) REVERT: E 88 MET cc_start: 0.7981 (ptp) cc_final: 0.7560 (ptt) REVERT: E 179 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7586 (ttm170) REVERT: E 241 GLU cc_start: 0.6852 (mp0) cc_final: 0.6585 (mp0) REVERT: E 345 ASP cc_start: 0.8606 (m-30) cc_final: 0.7933 (m-30) REVERT: B 134 SER cc_start: 0.8218 (p) cc_final: 0.7774 (t) REVERT: B 179 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7577 (ttm170) REVERT: B 238 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8409 (mptp) REVERT: B 258 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8019 (ttmt) REVERT: B 345 ASP cc_start: 0.8619 (m-30) cc_final: 0.7971 (m-30) REVERT: C 88 MET cc_start: 0.7935 (ptp) cc_final: 0.7642 (ptt) REVERT: C 134 SER cc_start: 0.8318 (p) cc_final: 0.7903 (t) REVERT: C 179 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7812 (ttm170) REVERT: C 238 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8295 (mptp) REVERT: C 457 LYS cc_start: 0.8371 (mtmt) cc_final: 0.7949 (mmtt) REVERT: D 88 MET cc_start: 0.7925 (ptp) cc_final: 0.7651 (ptt) REVERT: D 179 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7709 (ttm170) REVERT: D 241 GLU cc_start: 0.7598 (tt0) cc_final: 0.7189 (mp0) REVERT: D 457 LYS cc_start: 0.8277 (tptt) cc_final: 0.7897 (mmtt) outliers start: 37 outliers final: 22 residues processed: 232 average time/residue: 1.4950 time to fit residues: 375.1277 Evaluate side-chains 231 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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 A residue 335 MET Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 235 ASP 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 238 LYS 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 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: 8.9990 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.159410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131611 restraints weight = 14011.782| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.23 r_work: 0.3051 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3299 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 : 0.783 20.764 19785 Z= 0.402 Chirality : 0.050 0.456 2235 Planarity : 0.006 0.052 2380 Dihedral : 7.499 56.516 2425 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.66 % Allowed : 11.69 % Favored : 85.65 % 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: 2.37 (0.22), residues: 530 sheet: 1.21 (0.24), residues: 440 loop : -0.16 (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 0.004 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01529 ( 10) link_NAG-ASN : angle 9.76568 ( 30) hydrogen bonds : bond 0.09861 ( 670) hydrogen bonds : angle 4.56376 ( 2100) SS BOND : bond 0.01118 ( 4) SS BOND : angle 1.71628 ( 10) covalent geometry : bond 0.00404 (14610) covalent geometry : angle 0.68433 (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 251 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 1.500 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.7989 (ptp) cc_final: 0.7626 (ptt) REVERT: A 134 SER cc_start: 0.8211 (p) cc_final: 0.7792 (t) REVERT: A 181 GLN cc_start: 0.8530 (mm110) cc_final: 0.7988 (mt0) REVERT: A 227 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7635 (tmt) REVERT: A 238 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8365 (mptp) REVERT: A 457 LYS cc_start: 0.8397 (mmtp) cc_final: 0.7972 (mmtt) REVERT: E 88 MET cc_start: 0.8005 (ptp) cc_final: 0.7597 (ptt) REVERT: E 179 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7616 (ttm170) REVERT: E 238 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8291 (mptp) REVERT: E 241 GLU cc_start: 0.6904 (mp0) cc_final: 0.6657 (mp0) REVERT: B 134 SER cc_start: 0.8272 (p) cc_final: 0.7809 (t) REVERT: B 179 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7597 (ttm170) REVERT: C 88 MET cc_start: 0.7971 (ptp) cc_final: 0.7702 (ptt) REVERT: C 179 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7901 (ttm170) REVERT: C 238 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8294 (mptp) REVERT: C 457 LYS cc_start: 0.8405 (mtmt) cc_final: 0.7965 (mmtt) REVERT: D 88 MET cc_start: 0.7976 (ptp) cc_final: 0.7393 (ppp) REVERT: D 179 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7762 (ttm170) REVERT: D 238 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8314 (mptp) REVERT: D 241 GLU cc_start: 0.7649 (tt0) cc_final: 0.7247 (mp0) REVERT: D 457 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7919 (mmtt) outliers start: 41 outliers final: 19 residues processed: 238 average time/residue: 1.5743 time to fit residues: 403.9666 Evaluate side-chains 219 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 1.842 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 162 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 247 GLN E 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.158971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131216 restraints weight = 14031.173| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.23 r_work: 0.3046 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3357 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= 0.221 Angle : 0.786 20.662 19785 Z= 0.404 Chirality : 0.050 0.454 2235 Planarity : 0.006 0.051 2380 Dihedral : 7.417 58.821 2425 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.27 % Allowed : 12.47 % 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: 1.55 (0.20), residues: 1640 helix: 2.37 (0.22), residues: 530 sheet: 1.22 (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 0.021 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 0.01562 ( 10) link_NAG-ASN : angle 9.76418 ( 30) hydrogen bonds : bond 0.09888 ( 670) hydrogen bonds : angle 4.55060 ( 2100) SS BOND : bond 0.01112 ( 4) SS BOND : angle 1.72677 ( 10) covalent geometry : bond 0.00406 (14610) covalent geometry : angle 0.68711 (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 229 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.8002 (ptp) cc_final: 0.7659 (ptt) REVERT: A 134 SER cc_start: 0.8231 (p) cc_final: 0.7811 (t) REVERT: A 181 GLN cc_start: 0.8537 (mm110) cc_final: 0.7988 (mt0) REVERT: A 225 ASP cc_start: 0.8080 (m-30) cc_final: 0.7821 (m-30) REVERT: A 227 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7637 (tmt) REVERT: A 457 LYS cc_start: 0.8396 (mmtp) cc_final: 0.7971 (mmtt) REVERT: E 88 MET cc_start: 0.8026 (ptp) cc_final: 0.7617 (ptt) REVERT: E 179 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7617 (ttm170) REVERT: E 238 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8327 (mptp) REVERT: E 241 GLU cc_start: 0.6889 (mp0) cc_final: 0.6645 (mp0) REVERT: B 134 SER cc_start: 0.8296 (p) cc_final: 0.7830 (t) REVERT: B 179 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7582 (ttm170) REVERT: C 88 MET cc_start: 0.7994 (ptp) cc_final: 0.7730 (ptt) REVERT: C 134 SER cc_start: 0.8493 (p) cc_final: 0.8024 (t) REVERT: C 179 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7937 (ttm170) REVERT: C 225 ASP cc_start: 0.8049 (m-30) cc_final: 0.7845 (m-30) REVERT: C 238 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8321 (mptp) REVERT: C 457 LYS cc_start: 0.8391 (mtmt) cc_final: 0.7952 (mmtt) REVERT: D 88 MET cc_start: 0.7977 (ptp) cc_final: 0.7688 (ptt) REVERT: D 179 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7757 (ttm170) REVERT: D 238 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8325 (mptp) REVERT: D 241 GLU cc_start: 0.7639 (tt0) cc_final: 0.7211 (mp0) REVERT: D 457 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7913 (mmtt) outliers start: 35 outliers final: 20 residues processed: 221 average time/residue: 1.4971 time to fit residues: 358.3978 Evaluate side-chains 215 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 30 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 144 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.159906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132144 restraints weight = 13996.972| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.23 r_work: 0.3042 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3411 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= 0.208 Angle : 0.764 20.860 19785 Z= 0.391 Chirality : 0.049 0.458 2235 Planarity : 0.006 0.050 2380 Dihedral : 7.237 59.169 2425 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.40 % Allowed : 12.47 % Favored : 85.13 % 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: 2.41 (0.22), residues: 530 sheet: 1.22 (0.24), residues: 440 loop : -0.18 (0.21), 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 0.01594 ( 10) link_NAG-ASN : angle 9.75440 ( 30) hydrogen bonds : bond 0.09429 ( 670) hydrogen bonds : angle 4.49994 ( 2100) SS BOND : bond 0.01056 ( 4) SS BOND : angle 1.63301 ( 10) covalent geometry : bond 0.00377 (14610) covalent geometry : angle 0.66218 (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 225 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7985 (ptp) cc_final: 0.7630 (OUTLIER) REVERT: A 134 SER cc_start: 0.8203 (p) cc_final: 0.7789 (t) REVERT: A 181 GLN cc_start: 0.8521 (mm110) cc_final: 0.7970 (mt0) REVERT: A 225 ASP cc_start: 0.8076 (m-30) cc_final: 0.7783 (m-30) REVERT: A 227 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7597 (tmt) REVERT: A 238 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8379 (mptp) REVERT: E 88 MET cc_start: 0.8012 (ptp) cc_final: 0.7589 (ptt) REVERT: E 179 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7641 (ttm170) REVERT: E 238 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8322 (mptp) REVERT: B 134 SER cc_start: 0.8251 (p) cc_final: 0.7791 (t) REVERT: B 179 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7589 (ttm170) REVERT: C 88 MET cc_start: 0.7996 (ptp) cc_final: 0.7721 (ptt) REVERT: C 134 SER cc_start: 0.8407 (p) cc_final: 0.7946 (t) REVERT: C 179 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7890 (ttm170) REVERT: C 225 ASP cc_start: 0.8027 (m-30) cc_final: 0.7825 (m-30) REVERT: C 238 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8310 (mptp) REVERT: C 241 GLU cc_start: 0.7586 (tt0) cc_final: 0.7181 (mp0) REVERT: C 457 LYS cc_start: 0.8365 (mtmt) cc_final: 0.7928 (mmtt) REVERT: D 88 MET cc_start: 0.7998 (ptp) cc_final: 0.7693 (ptt) REVERT: D 179 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7737 (ttm170) REVERT: D 238 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8307 (mptp) REVERT: D 241 GLU cc_start: 0.7635 (tt0) cc_final: 0.7228 (mp0) REVERT: D 457 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7879 (mmtt) outliers start: 37 outliers final: 23 residues processed: 219 average time/residue: 1.3485 time to fit residues: 321.8566 Evaluate side-chains 218 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 238 LYS 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 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: 0.6980 chunk 89 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 21 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 chunk 139 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 GLN D 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.167005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140222 restraints weight = 14152.928| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.23 r_work: 0.3499 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14624 Z= 0.142 Angle : 0.643 20.368 19785 Z= 0.317 Chirality : 0.046 0.464 2235 Planarity : 0.005 0.048 2380 Dihedral : 6.206 56.047 2425 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.75 % Allowed : 13.25 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.20), residues: 1640 helix: 2.72 (0.22), residues: 535 sheet: 0.94 (0.24), residues: 465 loop : 0.08 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 349 HIS 0.005 0.001 HIS B 254 PHE 0.016 0.001 PHE A 356 TYR 0.016 0.002 TYR D 340 ARG 0.002 0.000 ARG E 191 Details of bonding type rmsd link_NAG-ASN : bond 0.01752 ( 10) link_NAG-ASN : angle 9.61231 ( 30) hydrogen bonds : bond 0.06564 ( 670) hydrogen bonds : angle 4.19164 ( 2100) SS BOND : bond 0.00485 ( 4) SS BOND : angle 0.76570 ( 10) covalent geometry : bond 0.00229 (14610) covalent geometry : angle 0.52246 (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 224 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7890 (ptp) cc_final: 0.7556 (OUTLIER) REVERT: A 227 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7537 (tmt) REVERT: A 345 ASP cc_start: 0.8253 (m-30) cc_final: 0.7959 (m-30) REVERT: E 88 MET cc_start: 0.8015 (ptp) cc_final: 0.7654 (ptt) REVERT: E 179 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7552 (ttm170) REVERT: E 241 GLU cc_start: 0.6967 (mp0) cc_final: 0.6715 (mp0) REVERT: B 345 ASP cc_start: 0.8295 (m-30) cc_final: 0.8051 (m-30) REVERT: C 88 MET cc_start: 0.7972 (ptp) cc_final: 0.7686 (ptt) REVERT: C 134 SER cc_start: 0.8299 (p) cc_final: 0.7861 (t) REVERT: C 179 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7686 (ttm170) REVERT: C 457 LYS cc_start: 0.8262 (mtmt) cc_final: 0.7882 (mmtm) REVERT: D 88 MET cc_start: 0.7745 (ptp) cc_final: 0.7427 (ptt) REVERT: D 179 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7693 (ttm170) REVERT: D 238 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8274 (mptp) REVERT: D 241 GLU cc_start: 0.7579 (tt0) cc_final: 0.7350 (mp0) REVERT: D 345 ASP cc_start: 0.8324 (m-30) cc_final: 0.7681 (m-30) REVERT: D 457 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7870 (mmtt) outliers start: 27 outliers final: 14 residues processed: 218 average time/residue: 1.8325 time to fit residues: 435.7977 Evaluate side-chains 210 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 2.079 ------------------------------------------------------------------------------- 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 122 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 111 optimal weight: 0.0970 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: 5.9990 chunk 153 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 GLN E 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.164703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137774 restraints weight = 13311.082| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.18 r_work: 0.3043 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14624 Z= 0.233 Angle : 0.811 20.832 19785 Z= 0.417 Chirality : 0.051 0.483 2235 Planarity : 0.006 0.051 2380 Dihedral : 7.257 58.673 2425 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.43 % Allowed : 14.09 % 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: 1.62 (0.20), residues: 1640 helix: 2.47 (0.22), residues: 530 sheet: 1.26 (0.24), residues: 440 loop : -0.18 (0.21), 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 0.002 PHE B 356 TYR 0.016 0.002 TYR A 362 ARG 0.004 0.001 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01642 ( 10) link_NAG-ASN : angle 9.76192 ( 30) hydrogen bonds : bond 0.10157 ( 670) hydrogen bonds : angle 4.54053 ( 2100) SS BOND : bond 0.01478 ( 4) SS BOND : angle 3.07864 ( 10) covalent geometry : bond 0.00442 (14610) covalent geometry : angle 0.71334 (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: 22 poor density : 194 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7931 (ptp) cc_final: 0.7569 (OUTLIER) REVERT: A 134 SER cc_start: 0.8200 (p) cc_final: 0.7794 (t) REVERT: A 181 GLN cc_start: 0.8516 (mm110) cc_final: 0.7948 (mt0) REVERT: A 225 ASP cc_start: 0.8094 (m-30) cc_final: 0.7839 (m-30) REVERT: A 227 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7592 (tmt) REVERT: E 88 MET cc_start: 0.7988 (ptp) cc_final: 0.7571 (ptt) REVERT: E 179 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7647 (ttm170) REVERT: E 345 ASP cc_start: 0.8566 (m-30) cc_final: 0.8014 (m-30) REVERT: B 134 SER cc_start: 0.8253 (p) cc_final: 0.7813 (t) REVERT: B 457 LYS cc_start: 0.8239 (tptt) cc_final: 0.7890 (mmtt) REVERT: C 88 MET cc_start: 0.7995 (ptp) cc_final: 0.7712 (ptt) REVERT: C 134 SER cc_start: 0.8441 (p) cc_final: 0.7983 (t) REVERT: C 179 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7879 (ttm170) REVERT: C 457 LYS cc_start: 0.8384 (mtmt) cc_final: 0.7958 (mmtt) REVERT: D 88 MET cc_start: 0.7941 (ptp) cc_final: 0.7669 (ptt) REVERT: D 179 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7765 (ttm170) REVERT: D 238 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8322 (mptp) REVERT: D 241 GLU cc_start: 0.7638 (tt0) cc_final: 0.7294 (mp0) REVERT: D 457 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7905 (mmtt) outliers start: 22 outliers final: 15 residues processed: 212 average time/residue: 1.4358 time to fit residues: 330.2411 Evaluate side-chains 198 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 334 SER Chi-restraints excluded: chain B residue 122 LEU 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 334 SER 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 190 LEU Chi-restraints excluded: chain D residue 238 LYS 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 112 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 GLN D 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.168641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.142244 restraints weight = 13748.520| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.19 r_work: 0.3122 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14624 Z= 0.168 Angle : 0.698 20.541 19785 Z= 0.350 Chirality : 0.047 0.488 2235 Planarity : 0.005 0.048 2380 Dihedral : 6.625 56.011 2425 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.43 % Allowed : 14.09 % 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: 1.73 (0.20), residues: 1640 helix: 2.63 (0.22), residues: 530 sheet: 1.16 (0.24), residues: 440 loop : -0.05 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 349 HIS 0.005 0.001 HIS C 254 PHE 0.017 0.002 PHE B 356 TYR 0.014 0.002 TYR D 340 ARG 0.001 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01718 ( 10) link_NAG-ASN : angle 9.65210 ( 30) hydrogen bonds : bond 0.07944 ( 670) hydrogen bonds : angle 4.36976 ( 2100) SS BOND : bond 0.01314 ( 4) SS BOND : angle 0.97864 ( 10) covalent geometry : bond 0.00281 (14610) covalent geometry : angle 0.58793 (19745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12279.62 seconds wall clock time: 212 minutes 5.04 seconds (12725.04 seconds total)