Starting phenix.real_space_refine on Thu Feb 5 00:49:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rh4_19167/02_2026/8rh4_19167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rh4_19167/02_2026/8rh4_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_19167/02_2026/8rh4_19167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rh4_19167/02_2026/8rh4_19167.map" model { file = "/net/cci-nas-00/data/ceres_data/8rh4_19167/02_2026/8rh4_19167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rh4_19167/02_2026/8rh4_19167.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14292 Number of models: 1 Model: "" Number of chains: 15 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: "B" 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: "D" 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} Time building chain proxies: 3.71, per 1000 atoms: 0.26 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=5, 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 C 198 " - pdb=" SG CYS C 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: 1.41 Conformation dependent library (CDL) restraints added in 561.8 milliseconds 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: 0.48 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: 2.47 Time building geometry restraints manager: 1.79 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: 8355 17.96 - 35.92: 400 35.92 - 53.88: 55 53.88 - 71.84: 25 71.84 - 89.80: 15 Dihedral angle restraints: 8850 sinusoidal: 3895 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 8847 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: 2.39 - 2.89: 5138 2.89 - 3.39: 11882 3.39 - 3.90: 22049 3.90 - 4.40: 26918 4.40 - 4.90: 44798 Nonbonded interactions: 110785 Sorted by model distance: 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 nonbonded pdb=" CG ASN B 140 " pdb=" O5 NAG B 501 " model vdw 2.389 2.616 ... (remaining 110780 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: 7.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.680 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:9.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.950 ------------------------------------------------------------------------------- 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 14625 Z= 0.575 Angle : 1.472 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 : 2.388 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.027 0.004 ARG D 307 TYR 0.046 0.010 TYR C 272 PHE 0.046 0.007 PHE D 290 TRP 0.032 0.009 TRP C 128 HIS 0.010 0.004 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00990 (14610) covalent geometry : angle 1.26118 (19745) SS BOND : bond 0.01080 ( 5) SS BOND : angle 2.10284 ( 10) hydrogen bonds : bond 0.19231 ( 670) hydrogen bonds : angle 6.49260 ( 2100) link_NAG-ASN : bond 0.15129 ( 10) link_NAG-ASN : angle 19.48825 ( 30) *********************** 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 : 0.610 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: 0.8626 (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: 0.7567 time to fit residues: 230.0260 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 : 0.405 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3584 r_free = 0.3584 target = 0.145459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119136 restraints weight = 12500.018| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.09 r_work: 0.3080 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14625 Z= 0.224 Angle : 0.893 25.902 19785 Z= 0.441 Chirality : 0.053 0.514 2235 Planarity : 0.007 0.062 2380 Dihedral : 8.220 76.899 2427 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.75 % Allowed : 6.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1640 helix: 1.75 (0.23), residues: 535 sheet: 1.40 (0.24), residues: 445 loop : 0.03 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 191 TYR 0.016 0.002 TYR A 188 PHE 0.032 0.002 PHE A 290 TRP 0.013 0.002 TRP A 349 HIS 0.006 0.002 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00412 (14610) covalent geometry : angle 0.75424 (19745) SS BOND : bond 0.01078 ( 5) SS BOND : angle 2.18631 ( 10) hydrogen bonds : bond 0.09814 ( 670) hydrogen bonds : angle 4.79794 ( 2100) link_NAG-ASN : bond 0.00441 ( 10) link_NAG-ASN : angle 12.24296 ( 30) *********************** 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 259 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 SER cc_start: 0.8220 (p) cc_final: 0.7800 (t) REVERT: A 174 ASP cc_start: 0.8280 (m-30) cc_final: 0.8025 (m-30) REVERT: E 179 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7601 (ttm170) REVERT: E 241 GLU cc_start: 0.7372 (tt0) cc_final: 0.6996 (mp0) REVERT: B 134 SER cc_start: 0.8357 (p) cc_final: 0.7848 (t) REVERT: B 179 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7615 (ttm170) REVERT: B 241 GLU cc_start: 0.7226 (tt0) cc_final: 0.6889 (mp0) REVERT: B 373 GLU cc_start: 0.6136 (mt-10) cc_final: 0.5738 (mp0) REVERT: C 134 SER cc_start: 0.8364 (p) cc_final: 0.7928 (t) REVERT: C 179 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7787 (ttm170) REVERT: C 295 MET cc_start: 0.8723 (mmm) cc_final: 0.8508 (mmp) REVERT: C 373 GLU cc_start: 0.6191 (mt-10) cc_final: 0.5815 (mp0) REVERT: C 457 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7911 (mmtp) REVERT: D 179 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7713 (ttm170) REVERT: D 241 GLU cc_start: 0.7355 (tt0) cc_final: 0.6939 (mp0) outliers start: 27 outliers final: 9 residues processed: 248 average time/residue: 0.7391 time to fit residues: 197.5923 Evaluate side-chains 219 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 238 LYS 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 C residue 179 ARG 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 104 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 136 optimal weight: 0.2980 chunk 129 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 132 optimal weight: 0.0870 chunk 108 optimal weight: 3.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN C 247 GLN D 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.169696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.143260 restraints weight = 13952.708| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.20 r_work: 0.3138 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14625 Z= 0.156 Angle : 0.706 22.194 19785 Z= 0.345 Chirality : 0.049 0.526 2235 Planarity : 0.005 0.052 2380 Dihedral : 6.813 71.904 2425 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.88 % Allowed : 8.77 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.20), residues: 1640 helix: 2.34 (0.23), residues: 535 sheet: 1.06 (0.23), residues: 485 loop : 0.09 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 191 TYR 0.014 0.002 TYR D 340 PHE 0.023 0.002 PHE B 290 TRP 0.013 0.001 TRP A 349 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00252 (14610) covalent geometry : angle 0.56957 (19745) SS BOND : bond 0.00548 ( 5) SS BOND : angle 1.00774 ( 10) hydrogen bonds : bond 0.07468 ( 670) hydrogen bonds : angle 4.39319 ( 2100) link_NAG-ASN : bond 0.01434 ( 10) link_NAG-ASN : angle 10.70366 ( 30) *********************** 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 250 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.7797 (ptp) cc_final: 0.7348 (ptt) REVERT: A 134 SER cc_start: 0.8115 (p) cc_final: 0.7729 (t) REVERT: A 227 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7499 (tmt) REVERT: A 238 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8234 (mptp) REVERT: A 241 GLU cc_start: 0.7508 (tt0) cc_final: 0.7225 (mp0) REVERT: A 345 ASP cc_start: 0.8405 (m-30) cc_final: 0.8052 (m-30) REVERT: E 181 GLN cc_start: 0.8386 (mm110) cc_final: 0.7989 (mt0) REVERT: E 227 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7348 (tmt) REVERT: E 238 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8168 (mptp) REVERT: E 345 ASP cc_start: 0.8332 (m-30) cc_final: 0.8020 (m-30) REVERT: B 134 SER cc_start: 0.8153 (p) cc_final: 0.7732 (t) REVERT: B 241 GLU cc_start: 0.7347 (tt0) cc_final: 0.6970 (mp0) REVERT: B 345 ASP cc_start: 0.8440 (m-30) cc_final: 0.8111 (m-30) REVERT: B 373 GLU cc_start: 0.5953 (mt-10) cc_final: 0.5580 (mp0) REVERT: C 134 SER cc_start: 0.8299 (p) cc_final: 0.7897 (t) REVERT: C 295 MET cc_start: 0.8634 (mmm) cc_final: 0.8384 (mmp) REVERT: C 324 MET cc_start: 0.9110 (tpt) cc_final: 0.8876 (tpp) REVERT: C 345 ASP cc_start: 0.8338 (m-30) cc_final: 0.7982 (m-30) REVERT: C 373 GLU cc_start: 0.5957 (mt-10) cc_final: 0.5558 (mp0) REVERT: D 238 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8164 (mptp) REVERT: D 241 GLU cc_start: 0.7506 (tt0) cc_final: 0.7102 (mp0) REVERT: D 345 ASP cc_start: 0.8364 (m-30) cc_final: 0.7972 (m-30) REVERT: D 373 GLU cc_start: 0.6166 (mt-10) cc_final: 0.5747 (mp0) outliers start: 29 outliers final: 15 residues processed: 239 average time/residue: 0.6763 time to fit residues: 175.1903 Evaluate side-chains 228 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 178 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 E residue 177 MET Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 122 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 42 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 117 optimal weight: 0.0970 chunk 25 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.155991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125922 restraints weight = 13961.477| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.29 r_work: 0.3030 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14625 Z= 0.206 Angle : 0.774 21.689 19785 Z= 0.391 Chirality : 0.050 0.491 2235 Planarity : 0.006 0.054 2380 Dihedral : 7.286 68.512 2425 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.47 % Allowed : 10.45 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.20), residues: 1640 helix: 2.37 (0.22), residues: 530 sheet: 1.03 (0.24), residues: 470 loop : 0.05 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 270 TYR 0.014 0.002 TYR A 362 PHE 0.020 0.002 PHE B 356 TRP 0.011 0.002 TRP C 230 HIS 0.006 0.002 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00367 (14610) covalent geometry : angle 0.66091 (19745) SS BOND : bond 0.00880 ( 5) SS BOND : angle 1.67856 ( 10) hydrogen bonds : bond 0.09422 ( 670) hydrogen bonds : angle 4.55849 ( 2100) link_NAG-ASN : bond 0.01596 ( 10) link_NAG-ASN : angle 10.31588 ( 30) *********************** 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 251 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7940 (ptp) cc_final: 0.7494 (ptt) REVERT: A 134 SER cc_start: 0.8166 (p) cc_final: 0.7761 (t) REVERT: A 227 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7559 (tmt) REVERT: A 238 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8342 (mptp) REVERT: A 241 GLU cc_start: 0.7567 (tt0) cc_final: 0.7291 (mp0) REVERT: E 179 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7603 (ttm170) REVERT: E 345 ASP cc_start: 0.8604 (m-30) cc_final: 0.8054 (m-30) REVERT: B 134 SER cc_start: 0.8184 (p) cc_final: 0.7731 (t) REVERT: B 179 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7593 (ttm170) REVERT: B 241 GLU cc_start: 0.7546 (tt0) cc_final: 0.7107 (mp0) REVERT: B 345 ASP cc_start: 0.8639 (m-30) cc_final: 0.8066 (m-30) REVERT: C 134 SER cc_start: 0.8315 (p) cc_final: 0.7904 (t) REVERT: C 179 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7832 (ttm170) REVERT: C 238 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8316 (mptp) REVERT: C 295 MET cc_start: 0.8696 (mmm) cc_final: 0.8451 (mmp) REVERT: C 457 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7909 (mmtt) REVERT: D 88 MET cc_start: 0.7855 (ptp) cc_final: 0.7406 (ptt) REVERT: D 179 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7712 (ttm170) REVERT: D 241 GLU cc_start: 0.7605 (tt0) cc_final: 0.7140 (mp0) REVERT: D 295 MET cc_start: 0.8970 (mmp) cc_final: 0.8636 (mmp) outliers start: 38 outliers final: 18 residues processed: 237 average time/residue: 0.7672 time to fit residues: 196.2728 Evaluate side-chains 235 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 178 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 E residue 122 LEU Chi-restraints excluded: chain E residue 177 MET 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 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 334 SER Chi-restraints excluded: chain C residue 335 MET 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 335 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 163 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 139 optimal weight: 0.0770 chunk 18 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.167493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140656 restraints weight = 14058.828| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.22 r_work: 0.3483 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14625 Z= 0.142 Angle : 0.648 20.542 19785 Z= 0.318 Chirality : 0.047 0.471 2235 Planarity : 0.005 0.048 2380 Dihedral : 6.479 60.212 2425 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.82 % Allowed : 11.95 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.20), residues: 1640 helix: 2.63 (0.22), residues: 535 sheet: 0.93 (0.24), residues: 485 loop : 0.14 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 191 TYR 0.014 0.002 TYR E 272 PHE 0.017 0.001 PHE B 290 TRP 0.012 0.001 TRP D 128 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00231 (14610) covalent geometry : angle 0.52396 (19745) SS BOND : bond 0.00766 ( 5) SS BOND : angle 0.91801 ( 10) hydrogen bonds : bond 0.06662 ( 670) hydrogen bonds : angle 4.21575 ( 2100) link_NAG-ASN : bond 0.01587 ( 10) link_NAG-ASN : angle 9.78602 ( 30) *********************** 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 249 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7743 (ptp) cc_final: 0.7366 (ptt) REVERT: A 181 GLN cc_start: 0.8469 (mm110) cc_final: 0.7957 (mt0) REVERT: A 227 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7598 (tmt) REVERT: A 345 ASP cc_start: 0.8273 (m-30) cc_final: 0.7980 (m-30) REVERT: A 457 LYS cc_start: 0.8331 (mmtp) cc_final: 0.7919 (mmtt) REVERT: E 88 MET cc_start: 0.7885 (ptp) cc_final: 0.7514 (ptt) REVERT: E 345 ASP cc_start: 0.8214 (m-30) cc_final: 0.7940 (m-30) REVERT: B 134 SER cc_start: 0.8070 (p) cc_final: 0.7696 (t) REVERT: B 241 GLU cc_start: 0.7435 (tt0) cc_final: 0.7210 (mp0) REVERT: B 345 ASP cc_start: 0.8269 (m-30) cc_final: 0.7996 (m-30) REVERT: C 134 SER cc_start: 0.8228 (p) cc_final: 0.7884 (t) REVERT: C 179 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7694 (ttm170) REVERT: C 227 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7219 (tmt) REVERT: C 345 ASP cc_start: 0.8246 (m-30) cc_final: 0.7895 (m-30) REVERT: C 373 GLU cc_start: 0.6128 (mt-10) cc_final: 0.5749 (mp0) REVERT: D 88 MET cc_start: 0.7760 (ptp) cc_final: 0.7396 (ptt) REVERT: D 179 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7669 (ttm170) REVERT: D 241 GLU cc_start: 0.7558 (tt0) cc_final: 0.7307 (mp0) REVERT: D 295 MET cc_start: 0.8813 (mmp) cc_final: 0.8450 (mmp) REVERT: D 345 ASP cc_start: 0.8242 (m-30) cc_final: 0.7928 (m-30) outliers start: 28 outliers final: 14 residues processed: 238 average time/residue: 0.7420 time to fit residues: 190.6527 Evaluate side-chains 237 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 334 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 126 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 137 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.163519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135894 restraints weight = 14072.962| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.24 r_work: 0.3115 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14625 Z= 0.170 Angle : 0.696 20.726 19785 Z= 0.348 Chirality : 0.048 0.445 2235 Planarity : 0.005 0.048 2380 Dihedral : 6.620 56.801 2425 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.95 % Allowed : 12.60 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.20), residues: 1640 helix: 2.70 (0.22), residues: 530 sheet: 1.28 (0.24), residues: 440 loop : 0.07 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 270 TYR 0.014 0.002 TYR A 362 PHE 0.017 0.002 PHE B 356 TRP 0.010 0.001 TRP C 230 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00292 (14610) covalent geometry : angle 0.58289 (19745) SS BOND : bond 0.00706 ( 5) SS BOND : angle 1.31012 ( 10) hydrogen bonds : bond 0.08056 ( 670) hydrogen bonds : angle 4.30013 ( 2100) link_NAG-ASN : bond 0.01595 ( 10) link_NAG-ASN : angle 9.77353 ( 30) *********************** 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 244 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7969 (ptp) cc_final: 0.7553 (ptt) REVERT: A 181 GLN cc_start: 0.8465 (mm110) cc_final: 0.7920 (mt0) REVERT: A 227 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7625 (tmt) REVERT: A 457 LYS cc_start: 0.8341 (mmtp) cc_final: 0.7914 (mmtt) REVERT: E 88 MET cc_start: 0.7990 (ptp) cc_final: 0.7562 (ptt) REVERT: E 179 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7601 (ttm170) REVERT: E 227 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7393 (tmt) REVERT: E 345 ASP cc_start: 0.8441 (m-30) cc_final: 0.8097 (m-30) REVERT: B 134 SER cc_start: 0.8103 (p) cc_final: 0.7724 (t) REVERT: B 241 GLU cc_start: 0.7607 (tt0) cc_final: 0.7163 (mp0) REVERT: B 345 ASP cc_start: 0.8516 (m-30) cc_final: 0.8162 (m-30) REVERT: C 88 MET cc_start: 0.7933 (ptp) cc_final: 0.7616 (ptt) REVERT: C 134 SER cc_start: 0.8206 (p) cc_final: 0.7859 (t) REVERT: C 179 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7679 (ttm170) REVERT: C 181 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7911 (mt0) REVERT: C 345 ASP cc_start: 0.8452 (m-30) cc_final: 0.7947 (m-30) REVERT: C 457 LYS cc_start: 0.8297 (mtmt) cc_final: 0.7843 (mmtt) REVERT: D 88 MET cc_start: 0.7857 (ptp) cc_final: 0.7460 (ptt) REVERT: D 179 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7697 (ttm170) REVERT: D 241 GLU cc_start: 0.7626 (tt0) cc_final: 0.7192 (mp0) REVERT: D 345 ASP cc_start: 0.8383 (m-30) cc_final: 0.8034 (m-30) outliers start: 30 outliers final: 19 residues processed: 237 average time/residue: 0.7363 time to fit residues: 188.2848 Evaluate side-chains 234 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 334 SER 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 256 THR Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 87 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 56 optimal weight: 0.1980 chunk 128 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.164176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136825 restraints weight = 13969.453| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.22 r_work: 0.3135 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14625 Z= 0.165 Angle : 0.680 20.116 19785 Z= 0.340 Chirality : 0.047 0.447 2235 Planarity : 0.005 0.047 2380 Dihedral : 6.528 47.316 2425 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.27 % Allowed : 12.40 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.20), residues: 1640 helix: 2.75 (0.22), residues: 530 sheet: 1.33 (0.25), residues: 430 loop : 0.11 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 270 TYR 0.014 0.002 TYR D 340 PHE 0.017 0.002 PHE B 356 TRP 0.011 0.001 TRP A 349 HIS 0.006 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00278 (14610) covalent geometry : angle 0.56958 (19745) SS BOND : bond 0.00678 ( 5) SS BOND : angle 1.16516 ( 10) hydrogen bonds : bond 0.07799 ( 670) hydrogen bonds : angle 4.24887 ( 2100) link_NAG-ASN : bond 0.01642 ( 10) link_NAG-ASN : angle 9.51666 ( 30) *********************** 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 250 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7929 (ptp) cc_final: 0.7548 (ptt) REVERT: A 181 GLN cc_start: 0.8454 (mm110) cc_final: 0.7923 (mt0) REVERT: A 227 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7645 (tmt) REVERT: A 457 LYS cc_start: 0.8303 (mmtp) cc_final: 0.7871 (mmtt) REVERT: E 88 MET cc_start: 0.7981 (ptp) cc_final: 0.7601 (ptt) REVERT: E 179 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7596 (ttm170) REVERT: E 227 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7430 (tmt) REVERT: E 345 ASP cc_start: 0.8413 (m-30) cc_final: 0.8060 (m-30) REVERT: B 134 SER cc_start: 0.8120 (p) cc_final: 0.7760 (t) REVERT: B 241 GLU cc_start: 0.7659 (tt0) cc_final: 0.7234 (mp0) REVERT: B 345 ASP cc_start: 0.8522 (m-30) cc_final: 0.8145 (m-30) REVERT: C 88 MET cc_start: 0.7934 (ptp) cc_final: 0.7647 (ptt) REVERT: C 179 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7679 (ttm170) REVERT: C 181 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7941 (mt0) REVERT: C 227 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7596 (tmt) REVERT: C 238 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8317 (mptp) REVERT: C 345 ASP cc_start: 0.8446 (m-30) cc_final: 0.7868 (m-30) REVERT: C 457 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7833 (mmtt) REVERT: D 88 MET cc_start: 0.7882 (ptp) cc_final: 0.7500 (ptt) REVERT: D 179 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7689 (ttm170) REVERT: D 241 GLU cc_start: 0.7592 (tt0) cc_final: 0.7180 (mp0) REVERT: D 295 MET cc_start: 0.8898 (mmp) cc_final: 0.8570 (mmp) REVERT: D 345 ASP cc_start: 0.8403 (m-30) cc_final: 0.7990 (m-30) outliers start: 35 outliers final: 20 residues processed: 239 average time/residue: 0.7558 time to fit residues: 194.8627 Evaluate side-chains 236 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 MET 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 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 256 THR Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 158 optimal weight: 0.1980 chunk 144 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.166163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139010 restraints weight = 14153.213| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.23 r_work: 0.3181 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14625 Z= 0.149 Angle : 0.649 20.195 19785 Z= 0.321 Chirality : 0.047 0.477 2235 Planarity : 0.005 0.045 2380 Dihedral : 6.191 48.803 2425 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.21 % Allowed : 12.60 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.20), residues: 1640 helix: 2.82 (0.22), residues: 535 sheet: 1.17 (0.24), residues: 455 loop : 0.12 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 270 TYR 0.014 0.002 TYR C 340 PHE 0.017 0.001 PHE A 356 TRP 0.011 0.001 TRP A 349 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00245 (14610) covalent geometry : angle 0.53381 (19745) SS BOND : bond 0.00550 ( 5) SS BOND : angle 1.08230 ( 10) hydrogen bonds : bond 0.07013 ( 670) hydrogen bonds : angle 4.12523 ( 2100) link_NAG-ASN : bond 0.01670 ( 10) link_NAG-ASN : angle 9.46965 ( 30) *********************** 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 247 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.7914 (ptp) cc_final: 0.7550 (ptt) REVERT: A 227 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7607 (tmt) REVERT: A 457 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7830 (mmtt) REVERT: E 88 MET cc_start: 0.8001 (ptp) cc_final: 0.7605 (ptt) REVERT: E 179 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7594 (ttm170) REVERT: E 227 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7436 (tmt) REVERT: E 345 ASP cc_start: 0.8306 (m-30) cc_final: 0.8038 (m-30) REVERT: B 76 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6618 (mt-10) REVERT: B 241 GLU cc_start: 0.7627 (tt0) cc_final: 0.7187 (mp0) REVERT: B 345 ASP cc_start: 0.8386 (m-30) cc_final: 0.8100 (m-30) REVERT: C 88 MET cc_start: 0.7896 (ptp) cc_final: 0.7607 (ptt) REVERT: C 179 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7674 (ttm170) REVERT: C 181 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7943 (mt0) REVERT: C 227 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7604 (tmt) REVERT: C 238 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8303 (mptp) REVERT: C 345 ASP cc_start: 0.8316 (m-30) cc_final: 0.7951 (m-30) REVERT: C 457 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7789 (mmtm) REVERT: D 88 MET cc_start: 0.7852 (ptp) cc_final: 0.7462 (ptt) REVERT: D 179 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7673 (ttm170) REVERT: D 241 GLU cc_start: 0.7588 (tt0) cc_final: 0.7181 (mp0) REVERT: D 295 MET cc_start: 0.8862 (mmp) cc_final: 0.8531 (mmp) REVERT: D 345 ASP cc_start: 0.8290 (m-30) cc_final: 0.8005 (m-30) outliers start: 34 outliers final: 19 residues processed: 234 average time/residue: 0.7697 time to fit residues: 194.2407 Evaluate side-chains 230 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain B residue 76 GLU 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 197 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 MET 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 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 256 THR Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 25 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 42 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.164945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137781 restraints weight = 13776.528| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.22 r_work: 0.3090 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14625 Z= 0.194 Angle : 0.735 20.393 19785 Z= 0.373 Chirality : 0.049 0.498 2235 Planarity : 0.005 0.047 2380 Dihedral : 6.823 52.715 2425 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.08 % Allowed : 12.99 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.20), residues: 1640 helix: 2.70 (0.22), residues: 530 sheet: 1.36 (0.25), residues: 430 loop : 0.02 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 270 TYR 0.015 0.002 TYR A 362 PHE 0.019 0.002 PHE B 356 TRP 0.010 0.002 TRP C 230 HIS 0.006 0.002 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00346 (14610) covalent geometry : angle 0.63261 (19745) SS BOND : bond 0.01029 ( 5) SS BOND : angle 2.46601 ( 10) hydrogen bonds : bond 0.08957 ( 670) hydrogen bonds : angle 4.35272 ( 2100) link_NAG-ASN : bond 0.01656 ( 10) link_NAG-ASN : angle 9.54570 ( 30) *********************** 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 235 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7944 (ptp) cc_final: 0.7571 (ptt) REVERT: A 181 GLN cc_start: 0.8493 (mm110) cc_final: 0.7921 (mt0) REVERT: A 227 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7640 (tmt) REVERT: A 335 MET cc_start: 0.7871 (tpp) cc_final: 0.7629 (mmm) REVERT: A 345 ASP cc_start: 0.8537 (m-30) cc_final: 0.7788 (m-30) REVERT: E 88 MET cc_start: 0.8042 (ptp) cc_final: 0.7649 (ptt) REVERT: E 179 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7626 (ttm170) REVERT: E 227 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7401 (tmt) REVERT: E 345 ASP cc_start: 0.8528 (m-30) cc_final: 0.8077 (m-30) REVERT: B 134 SER cc_start: 0.8194 (p) cc_final: 0.7822 (t) REVERT: B 241 GLU cc_start: 0.7663 (tt0) cc_final: 0.7228 (mp0) REVERT: B 345 ASP cc_start: 0.8597 (m-30) cc_final: 0.8105 (m-30) REVERT: B 457 LYS cc_start: 0.8235 (tptt) cc_final: 0.7868 (mmtt) REVERT: C 88 MET cc_start: 0.7955 (ptp) cc_final: 0.7682 (ptt) REVERT: C 134 SER cc_start: 0.8262 (p) cc_final: 0.7872 (t) REVERT: C 179 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7834 (ttm170) REVERT: C 227 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7592 (tmt) REVERT: C 238 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8307 (mptp) REVERT: C 457 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7877 (mmtt) REVERT: D 88 MET cc_start: 0.7934 (ptp) cc_final: 0.7640 (ptt) REVERT: D 179 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7706 (ttm170) REVERT: D 241 GLU cc_start: 0.7642 (tt0) cc_final: 0.7220 (mp0) REVERT: D 345 ASP cc_start: 0.8532 (m-30) cc_final: 0.8062 (m-30) outliers start: 32 outliers final: 15 residues processed: 226 average time/residue: 0.7585 time to fit residues: 184.9621 Evaluate side-chains 222 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 227 MET 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 227 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 33 optimal weight: 10.0000 chunk 144 optimal weight: 0.1980 chunk 154 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.163326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.135785 restraints weight = 14115.940| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.24 r_work: 0.3110 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14625 Z= 0.172 Angle : 0.697 20.202 19785 Z= 0.350 Chirality : 0.048 0.498 2235 Planarity : 0.005 0.048 2380 Dihedral : 6.740 58.331 2425 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.49 % Allowed : 13.90 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.20), residues: 1640 helix: 2.75 (0.22), residues: 530 sheet: 1.29 (0.25), residues: 430 loop : 0.07 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 270 TYR 0.013 0.002 TYR A 362 PHE 0.017 0.002 PHE B 356 TRP 0.010 0.001 TRP C 230 HIS 0.005 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00293 (14610) covalent geometry : angle 0.59050 (19745) SS BOND : bond 0.01110 ( 5) SS BOND : angle 1.21221 ( 10) hydrogen bonds : bond 0.08100 ( 670) hydrogen bonds : angle 4.29362 ( 2100) link_NAG-ASN : bond 0.01729 ( 10) link_NAG-ASN : angle 9.48448 ( 30) ********************** 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 220 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7953 (ptp) cc_final: 0.7586 (OUTLIER) REVERT: A 227 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7684 (tmt) REVERT: A 345 ASP cc_start: 0.8467 (m-30) cc_final: 0.7752 (m-30) REVERT: A 457 LYS cc_start: 0.8321 (mmtp) cc_final: 0.7889 (mmtt) REVERT: E 88 MET cc_start: 0.8032 (ptp) cc_final: 0.7641 (ptt) REVERT: E 179 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7597 (ttm170) REVERT: E 227 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7395 (tmt) REVERT: E 345 ASP cc_start: 0.8451 (m-30) cc_final: 0.8040 (m-30) REVERT: B 241 GLU cc_start: 0.7644 (tt0) cc_final: 0.7215 (mp0) REVERT: B 345 ASP cc_start: 0.8556 (m-30) cc_final: 0.8113 (m-30) REVERT: C 88 MET cc_start: 0.7972 (ptp) cc_final: 0.7688 (ptt) REVERT: C 179 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7819 (ttm170) REVERT: C 227 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7609 (tmt) REVERT: C 238 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8314 (mptp) REVERT: C 345 ASP cc_start: 0.8477 (m-30) cc_final: 0.7767 (m-30) REVERT: C 457 LYS cc_start: 0.8291 (mtmt) cc_final: 0.7845 (mmtt) REVERT: D 88 MET cc_start: 0.7920 (ptp) cc_final: 0.7537 (ptt) REVERT: D 179 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7674 (ttm170) REVERT: D 241 GLU cc_start: 0.7640 (tt0) cc_final: 0.7230 (mp0) REVERT: D 345 ASP cc_start: 0.8435 (m-30) cc_final: 0.7995 (m-30) outliers start: 23 outliers final: 16 residues processed: 215 average time/residue: 0.7619 time to fit residues: 176.7240 Evaluate side-chains 218 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 227 MET 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 227 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 134 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 145 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.165783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138701 restraints weight = 14004.355| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.23 r_work: 0.3164 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14625 Z= 0.152 Angle : 0.657 20.029 19785 Z= 0.327 Chirality : 0.047 0.497 2235 Planarity : 0.005 0.047 2380 Dihedral : 6.499 57.162 2425 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.49 % Allowed : 13.90 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.20), residues: 1640 helix: 2.82 (0.22), residues: 535 sheet: 1.13 (0.24), residues: 455 loop : 0.05 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 270 TYR 0.014 0.002 TYR C 340 PHE 0.017 0.002 PHE A 356 TRP 0.013 0.001 TRP A 349 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00253 (14610) covalent geometry : angle 0.54611 (19745) SS BOND : bond 0.00946 ( 5) SS BOND : angle 1.08523 ( 10) hydrogen bonds : bond 0.07155 ( 670) hydrogen bonds : angle 4.17083 ( 2100) link_NAG-ASN : bond 0.01697 ( 10) link_NAG-ASN : angle 9.38044 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5915.61 seconds wall clock time: 101 minutes 29.31 seconds (6089.31 seconds total)