Starting phenix.real_space_refine on Sat Oct 11 11:29:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rh4_19167/10_2025/8rh4_19167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rh4_19167/10_2025/8rh4_19167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rh4_19167/10_2025/8rh4_19167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rh4_19167/10_2025/8rh4_19167.map" model { file = "/net/cci-nas-00/data/ceres_data/8rh4_19167/10_2025/8rh4_19167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rh4_19167/10_2025/8rh4_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-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14292 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2741 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Chain: "E" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2741 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Chain: "C" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2741 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 139 Unusual residues: {' CL': 1, 'D10': 1, 'EST': 2, 'HEX': 6, 'NAG': 2, 'OCT': 3} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 92 Unusual residues: {'D10': 1, 'HEX': 5, 'NAG': 2, 'OCT': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 107 Unusual residues: {' CL': 1, 'D10': 1, 'EST': 1, 'HEX': 4, 'NAG': 2, 'OCT': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 112 Unusual residues: {'D10': 1, 'EST': 1, 'HEX': 5, 'NAG': 2, 'OCT': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 112 Unusual residues: {'D10': 1, 'EST': 1, 'HEX': 5, 'NAG': 2, 'OCT': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Restraints were copied for chains: B, D Time building chain proxies: 3.96, per 1000 atoms: 0.28 Number of scatterers: 14292 At special positions: 0 Unit cell: (92.805, 93.4775, 133.155, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 75 16.00 O 2565 8.00 N 2220 7.00 C 9430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 212 " distance=2.04 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 198 " distance=0.00 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 198 " distance=2.04 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 212 " distance=0.00 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 212 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM13862 O5 NAG E 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM13717 O5 NAG A 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM13948 O5 NAG B 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM14061 O5 NAG C 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14199 O5 NAG D 504 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 140 " " NAG A 502 " - " ASN A 234 " " NAG B 501 " - " ASN B 140 " " NAG B 502 " - " ASN B 234 " " NAG C 502 " - " ASN C 140 " " NAG C 503 " - " ASN C 234 " " NAG D 504 " - " ASN D 140 " " NAG D 505 " - " ASN D 234 " " NAG E 502 " - " ASN E 140 " " NAG E 503 " - " ASN E 234 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 622.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.46 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: 2.36 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3975 1.35 - 1.47: 4080 1.47 - 1.60: 6415 1.60 - 1.72: 0 1.72 - 1.85: 140 Bond restraints: 14610 Sorted by residual: bond pdb=" C HIS C 169 " pdb=" N ASP C 170 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.42e-02 4.96e+03 5.79e+00 bond pdb=" C HIS E 169 " pdb=" N ASP E 170 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.42e-02 4.96e+03 5.73e+00 bond pdb=" C HIS B 169 " pdb=" N ASP B 170 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.42e-02 4.96e+03 5.71e+00 bond pdb=" C HIS A 169 " pdb=" N ASP A 170 " ideal model delta sigma weight residual 1.332 1.365 -0.034 1.42e-02 4.96e+03 5.69e+00 bond pdb=" C HIS D 169 " pdb=" N ASP D 170 " ideal model delta sigma weight residual 1.332 1.365 -0.034 1.42e-02 4.96e+03 5.62e+00 ... (remaining 14605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 17637 1.92 - 3.85: 1754 3.85 - 5.77: 299 5.77 - 7.70: 45 7.70 - 9.62: 10 Bond angle restraints: 19745 Sorted by residual: angle pdb=" N PHE E 290 " pdb=" CA PHE E 290 " pdb=" CB PHE E 290 " ideal model delta sigma weight residual 110.42 104.78 5.64 1.18e+00 7.18e-01 2.28e+01 angle pdb=" N PHE D 290 " pdb=" CA PHE D 290 " pdb=" CB PHE D 290 " ideal model delta sigma weight residual 110.42 104.81 5.61 1.18e+00 7.18e-01 2.26e+01 angle pdb=" N PHE A 290 " pdb=" CA PHE A 290 " pdb=" CB PHE A 290 " ideal model delta sigma weight residual 110.42 104.82 5.60 1.18e+00 7.18e-01 2.25e+01 angle pdb=" N PHE C 290 " pdb=" CA PHE C 290 " pdb=" CB PHE C 290 " ideal model delta sigma weight residual 110.42 104.84 5.58 1.18e+00 7.18e-01 2.24e+01 angle pdb=" N PHE B 290 " pdb=" CA PHE B 290 " pdb=" CB PHE B 290 " ideal model delta sigma weight residual 110.42 104.87 5.55 1.18e+00 7.18e-01 2.22e+01 ... (remaining 19740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8353 17.96 - 35.92: 403 35.92 - 53.88: 55 53.88 - 71.84: 25 71.84 - 89.80: 15 Dihedral angle restraints: 8851 sinusoidal: 3896 harmonic: 4955 Sorted by residual: dihedral pdb=" CA LEU C 108 " pdb=" C LEU C 108 " pdb=" N ASP C 109 " pdb=" CA ASP C 109 " ideal model delta harmonic sigma weight residual 180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LEU E 108 " pdb=" C LEU E 108 " pdb=" N ASP E 109 " pdb=" CA ASP E 109 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU A 108 " pdb=" C LEU A 108 " pdb=" N ASP A 109 " pdb=" CA ASP A 109 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 8848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 2074 0.125 - 0.249: 136 0.249 - 0.374: 5 0.374 - 0.499: 5 0.499 - 0.624: 15 Chirality restraints: 2235 Sorted by residual: chirality pdb=" C1 NAG E 503 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 503 " pdb=" O5 NAG E 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.72e+00 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.67e+00 chirality pdb=" C1 NAG C 503 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 503 " pdb=" O5 NAG C 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.64e+00 ... (remaining 2232 not shown) Planarity restraints: 2390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.231 2.00e-02 2.50e+03 2.52e-01 7.91e+02 pdb=" CG ASN A 234 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.415 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " -0.290 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " -0.231 2.00e-02 2.50e+03 2.52e-01 7.91e+02 pdb=" CG ASN B 234 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " 0.415 2.00e-02 2.50e+03 pdb=" C1 NAG B 502 " -0.290 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " 0.231 2.00e-02 2.50e+03 2.51e-01 7.90e+02 pdb=" CG ASN C 234 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " -0.415 2.00e-02 2.50e+03 pdb=" C1 NAG C 503 " 0.290 2.00e-02 2.50e+03 ... (remaining 2387 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 41 2.61 - 3.19: 11176 3.19 - 3.76: 19375 3.76 - 4.33: 30857 4.33 - 4.90: 49339 Nonbonded interactions: 110788 Sorted by model distance: nonbonded pdb=" SG CYS C 198 " pdb=" SG CYS C 212 " model vdw 2.042 3.760 nonbonded pdb=" CG ASN C 140 " pdb=" O5 NAG C 502 " model vdw 2.388 2.616 nonbonded pdb=" CG ASN E 140 " pdb=" O5 NAG E 502 " model vdw 2.388 2.616 nonbonded pdb=" CG ASN A 140 " pdb=" O5 NAG A 501 " model vdw 2.389 2.616 nonbonded pdb=" CG ASN D 140 " pdb=" O5 NAG D 504 " model vdw 2.389 2.616 ... (remaining 110783 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 479 or resid 510)) selection = (chain 'B' and (resid 75 through 479 or resid 510)) selection = (chain 'C' and (resid 75 through 479 or resid 510)) selection = (chain 'D' and (resid 75 through 479 or resid 510)) selection = (chain 'E' and (resid 75 through 479 or resid 510)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.870 Find NCS groups from input model: 0.350 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:8.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.205 14624 Z= 0.575 Angle : 1.471 32.778 19785 Z= 0.736 Chirality : 0.086 0.624 2235 Planarity : 0.014 0.115 2380 Dihedral : 12.014 89.802 5615 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.32 % Allowed : 1.62 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 0.01070 ( 4) SS BOND : angle 1.88179 ( 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 : 0.569 Fit side-chains REVERT: A 174 ASP cc_start: 0.8410 (m-30) cc_final: 0.8144 (m-30) REVERT: A 345 ASP cc_start: 0.8732 (m-30) cc_final: 0.8529 (m-30) REVERT: E 88 MET cc_start: 0.7356 (ptp) cc_final: 0.7138 (ptt) REVERT: E 345 ASP cc_start: 0.8700 (m-30) cc_final: 0.8251 (m-30) REVERT: B 116 MET cc_start: 0.9152 (mtm) cc_final: 0.8884 (mtm) REVERT: B 345 ASP cc_start: 0.8739 (m-30) cc_final: 0.8341 (m-30) REVERT: C 88 MET cc_start: 0.7493 (ptp) cc_final: 0.7181 (ptt) REVERT: C 116 MET cc_start: 0.9058 (mtm) cc_final: 0.8810 (mtm) REVERT: C 178 LEU cc_start: 0.8872 (mt) cc_final: 0.8663 (tp) REVERT: C 225 ASP cc_start: 0.8094 (m-30) cc_final: 0.7889 (m-30) REVERT: C 345 ASP cc_start: 0.8627 (m-30) cc_final: 0.8418 (m-30) REVERT: D 88 MET cc_start: 0.7520 (ptp) cc_final: 0.7276 (ptt) outliers start: 5 outliers final: 1 residues processed: 282 average time/residue: 0.7373 time to fit residues: 224.2484 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 : 0.563 ------------------------------------------------------------------------------- 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 162 HIS C 199 ASN D 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.144766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114702 restraints weight = 12603.186| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.27 r_work: 0.3031 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14624 Z= 0.232 Angle : 0.898 25.191 19785 Z= 0.445 Chirality : 0.052 0.466 2235 Planarity : 0.007 0.061 2380 Dihedral : 8.202 76.821 2427 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.39 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 aren not related in a simple way. whole: 1.46 (0.20), residues: 1640 helix: 1.76 (0.23), residues: 535 sheet: 1.42 (0.24), residues: 445 loop : 0.05 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 307 TYR 0.016 0.003 TYR C 272 PHE 0.034 0.003 PHE A 290 TRP 0.014 0.002 TRP A 349 HIS 0.005 0.002 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00413 (14610) covalent geometry : angle 0.75988 (19745) SS BOND : bond 0.01090 ( 4) SS BOND : angle 2.04475 ( 10) hydrogen bonds : bond 0.09965 ( 670) hydrogen bonds : angle 4.81301 ( 2100) link_NAG-ASN : bond 0.01118 ( 10) link_NAG-ASN : angle 12.25161 ( 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 260 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 SER cc_start: 0.8165 (p) cc_final: 0.7773 (t) REVERT: A 174 ASP cc_start: 0.8326 (m-30) cc_final: 0.8053 (m-30) REVERT: E 179 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7640 (ttm170) REVERT: B 134 SER cc_start: 0.8333 (p) cc_final: 0.7848 (t) REVERT: B 179 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7662 (ttm170) REVERT: B 241 GLU cc_start: 0.7248 (tt0) cc_final: 0.6821 (mp0) REVERT: B 373 GLU cc_start: 0.6120 (mt-10) cc_final: 0.5686 (mp0) REVERT: C 134 SER cc_start: 0.8340 (p) cc_final: 0.7913 (t) REVERT: C 178 LEU cc_start: 0.8735 (mt) cc_final: 0.8535 (tp) REVERT: C 179 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7827 (ttm170) REVERT: C 373 GLU cc_start: 0.6196 (mt-10) cc_final: 0.5778 (mp0) REVERT: C 457 LYS cc_start: 0.8301 (mtmt) cc_final: 0.7903 (mmtt) REVERT: D 179 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7746 (ttm170) REVERT: D 241 GLU cc_start: 0.7391 (tt0) cc_final: 0.6915 (mp0) outliers start: 27 outliers final: 10 residues processed: 249 average time/residue: 0.7450 time to fit residues: 200.1118 Evaluate side-chains 220 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 104 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 132 optimal weight: 0.0770 chunk 108 optimal weight: 0.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.170383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.144067 restraints weight = 13939.324| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.20 r_work: 0.3165 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14624 Z= 0.153 Angle : 0.694 21.685 19785 Z= 0.339 Chirality : 0.048 0.504 2235 Planarity : 0.005 0.051 2380 Dihedral : 6.687 71.019 2425 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.69 % Allowed : 8.83 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.20), residues: 1640 helix: 2.40 (0.23), residues: 535 sheet: 0.96 (0.23), residues: 495 loop : 0.26 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 191 TYR 0.015 0.002 TYR D 340 PHE 0.024 0.002 PHE D 290 TRP 0.012 0.001 TRP A 349 HIS 0.004 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00247 (14610) covalent geometry : angle 0.55919 (19745) SS BOND : bond 0.00486 ( 4) SS BOND : angle 0.84942 ( 10) hydrogen bonds : bond 0.07198 ( 670) hydrogen bonds : angle 4.36168 ( 2100) link_NAG-ASN : bond 0.01479 ( 10) link_NAG-ASN : angle 10.56529 ( 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 248 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.7783 (ptp) cc_final: 0.7349 (ptt) REVERT: A 134 SER cc_start: 0.8116 (p) cc_final: 0.7744 (t) REVERT: A 174 ASP cc_start: 0.8294 (m-30) cc_final: 0.7996 (m-30) REVERT: A 227 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7494 (tmt) REVERT: A 238 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8214 (mptp) REVERT: A 241 GLU cc_start: 0.7497 (tt0) cc_final: 0.7236 (mp0) REVERT: A 345 ASP cc_start: 0.8327 (m-30) cc_final: 0.8038 (m-30) REVERT: E 181 GLN cc_start: 0.8397 (mm110) cc_final: 0.8002 (mt0) REVERT: E 227 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7346 (tmt) REVERT: E 241 GLU cc_start: 0.7400 (tt0) cc_final: 0.7094 (mp0) REVERT: E 345 ASP cc_start: 0.8307 (m-30) cc_final: 0.8068 (m-30) REVERT: B 134 SER cc_start: 0.8122 (p) cc_final: 0.7707 (t) REVERT: B 241 GLU cc_start: 0.7350 (tt0) cc_final: 0.6962 (mp0) REVERT: B 345 ASP cc_start: 0.8355 (m-30) cc_final: 0.8087 (m-30) REVERT: B 373 GLU cc_start: 0.5945 (mt-10) cc_final: 0.5607 (mp0) REVERT: C 134 SER cc_start: 0.8293 (p) cc_final: 0.7929 (t) REVERT: C 324 MET cc_start: 0.9108 (tpt) cc_final: 0.8871 (tpp) REVERT: C 345 ASP cc_start: 0.8309 (m-30) cc_final: 0.8046 (m-30) REVERT: C 373 GLU cc_start: 0.5914 (mt-10) cc_final: 0.5564 (mp0) REVERT: C 457 LYS cc_start: 0.8272 (mtmt) cc_final: 0.7853 (mmtt) REVERT: D 88 MET cc_start: 0.7714 (ptp) cc_final: 0.7346 (ptt) REVERT: D 238 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8189 (mptp) REVERT: D 241 GLU cc_start: 0.7523 (tt0) cc_final: 0.7104 (mp0) REVERT: D 345 ASP cc_start: 0.8344 (m-30) cc_final: 0.8006 (m-30) REVERT: D 373 GLU cc_start: 0.6148 (mt-10) cc_final: 0.5752 (mp0) outliers start: 26 outliers final: 13 residues processed: 237 average time/residue: 0.7038 time to fit residues: 180.9853 Evaluate side-chains 233 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain E residue 177 MET 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 122 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: 1.9990 chunk 158 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.163675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136652 restraints weight = 13831.764| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.19 r_work: 0.3052 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14624 Z= 0.215 Angle : 0.789 21.737 19785 Z= 0.400 Chirality : 0.051 0.489 2235 Planarity : 0.006 0.055 2380 Dihedral : 7.366 68.030 2425 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.47 % Allowed : 10.13 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.20), residues: 1640 helix: 2.35 (0.22), residues: 530 sheet: 1.28 (0.24), residues: 440 loop : -0.06 (0.20), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 270 TYR 0.014 0.002 TYR A 362 PHE 0.020 0.002 PHE E 290 TRP 0.011 0.002 TRP C 230 HIS 0.006 0.002 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00390 (14610) covalent geometry : angle 0.67844 (19745) SS BOND : bond 0.00936 ( 4) SS BOND : angle 1.63306 ( 10) hydrogen bonds : bond 0.09707 ( 670) hydrogen bonds : angle 4.58649 ( 2100) link_NAG-ASN : bond 0.01376 ( 10) link_NAG-ASN : angle 10.32859 ( 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 248 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.613 Fit side-chains REVERT: A 88 MET cc_start: 0.7965 (ptp) cc_final: 0.7535 (ptt) REVERT: A 134 SER cc_start: 0.8182 (p) cc_final: 0.7782 (t) REVERT: A 227 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7616 (tmt) REVERT: A 238 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8330 (mptp) REVERT: A 241 GLU cc_start: 0.7586 (tt0) cc_final: 0.7355 (mp0) REVERT: E 179 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7617 (ttm170) REVERT: E 238 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8310 (mptp) REVERT: E 345 ASP cc_start: 0.8603 (m-30) cc_final: 0.8073 (m-30) REVERT: B 134 SER cc_start: 0.8197 (p) cc_final: 0.7760 (t) REVERT: B 179 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7611 (ttm170) REVERT: B 241 GLU cc_start: 0.7574 (tt0) cc_final: 0.7173 (mp0) REVERT: B 345 ASP cc_start: 0.8637 (m-30) cc_final: 0.8054 (m-30) REVERT: C 134 SER cc_start: 0.8345 (p) cc_final: 0.7934 (t) REVERT: C 179 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7841 (ttm170) REVERT: C 238 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8324 (mptp) REVERT: C 457 LYS cc_start: 0.8392 (mtmt) cc_final: 0.8002 (mmtt) REVERT: D 88 MET cc_start: 0.7867 (ptp) cc_final: 0.7586 (ptt) REVERT: D 179 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7737 (ttm170) REVERT: D 241 GLU cc_start: 0.7650 (tt0) cc_final: 0.7254 (mp0) outliers start: 38 outliers final: 18 residues processed: 234 average time/residue: 0.7820 time to fit residues: 196.9984 Evaluate side-chains 231 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 37 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.164921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.137637 restraints weight = 14013.579| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.22 r_work: 0.3122 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14624 Z= 0.158 Angle : 0.679 20.764 19785 Z= 0.338 Chirality : 0.048 0.469 2235 Planarity : 0.005 0.049 2380 Dihedral : 6.833 61.045 2425 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.01 % Allowed : 11.95 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.20), residues: 1640 helix: 2.53 (0.22), residues: 535 sheet: 1.26 (0.24), residues: 440 loop : 0.01 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 270 TYR 0.014 0.002 TYR D 340 PHE 0.018 0.002 PHE D 290 TRP 0.012 0.001 TRP A 349 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00261 (14610) covalent geometry : angle 0.55968 (19745) SS BOND : bond 0.00753 ( 4) SS BOND : angle 1.12989 ( 10) hydrogen bonds : bond 0.07533 ( 670) hydrogen bonds : angle 4.32075 ( 2100) link_NAG-ASN : bond 0.01579 ( 10) link_NAG-ASN : angle 9.89116 ( 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 246 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7901 (ptp) cc_final: 0.7490 (ptt) REVERT: A 181 GLN cc_start: 0.8462 (mm110) cc_final: 0.7892 (mt0) REVERT: A 227 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7532 (tmt) REVERT: A 238 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8299 (mptp) REVERT: A 241 GLU cc_start: 0.7572 (tt0) cc_final: 0.7302 (mp0) REVERT: A 345 ASP cc_start: 0.8461 (m-30) cc_final: 0.8042 (m-30) REVERT: A 457 LYS cc_start: 0.8348 (mmtp) cc_final: 0.7924 (mmtt) REVERT: E 88 MET cc_start: 0.7931 (ptp) cc_final: 0.7507 (ptt) REVERT: E 179 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7548 (ttm170) REVERT: E 241 GLU cc_start: 0.7475 (tt0) cc_final: 0.7199 (mp0) REVERT: E 345 ASP cc_start: 0.8391 (m-30) cc_final: 0.8050 (m-30) REVERT: B 134 SER cc_start: 0.8083 (p) cc_final: 0.7693 (t) REVERT: B 241 GLU cc_start: 0.7570 (tt0) cc_final: 0.7144 (mp0) REVERT: B 345 ASP cc_start: 0.8447 (m-30) cc_final: 0.8082 (m-30) REVERT: C 134 SER cc_start: 0.8245 (p) cc_final: 0.7896 (t) REVERT: C 179 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7701 (ttm170) REVERT: C 227 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7168 (tmt) REVERT: C 238 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8253 (mptp) REVERT: C 345 ASP cc_start: 0.8425 (m-30) cc_final: 0.7905 (m-30) REVERT: C 457 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7847 (mmtt) REVERT: D 88 MET cc_start: 0.7833 (ptp) cc_final: 0.7409 (ptt) REVERT: D 179 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7666 (ttm170) REVERT: D 241 GLU cc_start: 0.7645 (tt0) cc_final: 0.7206 (mp0) REVERT: D 345 ASP cc_start: 0.8396 (m-30) cc_final: 0.7937 (m-30) outliers start: 31 outliers final: 15 residues processed: 234 average time/residue: 0.7434 time to fit residues: 187.3760 Evaluate side-chains 232 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 179 ARG 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 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: 0.8980 chunk 8 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.164548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137165 restraints weight = 14095.550| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.23 r_work: 0.3123 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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 0.023 14624 Z= 0.158 Angle : 0.672 20.252 19785 Z= 0.334 Chirality : 0.047 0.489 2235 Planarity : 0.005 0.047 2380 Dihedral : 6.527 50.731 2425 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.14 % Allowed : 12.40 % 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 aren not related in a simple way. whole: 1.90 (0.20), residues: 1640 helix: 2.75 (0.22), residues: 530 sheet: 1.26 (0.24), residues: 440 loop : 0.06 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 270 TYR 0.013 0.002 TYR D 340 PHE 0.017 0.002 PHE B 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 0.00263 (14610) covalent geometry : angle 0.55663 (19745) SS BOND : bond 0.00619 ( 4) SS BOND : angle 1.07200 ( 10) hydrogen bonds : bond 0.07577 ( 670) hydrogen bonds : angle 4.24884 ( 2100) link_NAG-ASN : bond 0.01589 ( 10) link_NAG-ASN : angle 9.66175 ( 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 249 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7909 (ptp) cc_final: 0.7532 (ptt) REVERT: A 181 GLN cc_start: 0.8454 (mm110) cc_final: 0.7903 (mt0) REVERT: A 227 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7626 (tmt) REVERT: A 345 ASP cc_start: 0.8471 (m-30) cc_final: 0.8124 (m-30) REVERT: A 457 LYS cc_start: 0.8298 (mmtp) cc_final: 0.7867 (mmtt) REVERT: E 88 MET cc_start: 0.7974 (ptp) cc_final: 0.7561 (ptt) REVERT: E 179 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7581 (ttm170) REVERT: E 227 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7383 (tmt) REVERT: E 241 GLU cc_start: 0.7498 (tt0) cc_final: 0.7251 (mp0) REVERT: E 345 ASP cc_start: 0.8376 (m-30) cc_final: 0.8097 (m-30) REVERT: B 134 SER cc_start: 0.8071 (p) cc_final: 0.7710 (t) REVERT: B 241 GLU cc_start: 0.7598 (tt0) cc_final: 0.7167 (mp0) REVERT: B 345 ASP cc_start: 0.8449 (m-30) cc_final: 0.8146 (m-30) REVERT: C 88 MET cc_start: 0.7927 (ptp) cc_final: 0.7635 (ptt) REVERT: C 179 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7663 (ttm170) REVERT: C 181 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7898 (mt0) REVERT: C 324 MET cc_start: 0.9051 (tpt) cc_final: 0.8828 (tpp) REVERT: C 345 ASP cc_start: 0.8381 (m-30) cc_final: 0.8013 (m-30) REVERT: C 457 LYS cc_start: 0.8280 (mtmt) cc_final: 0.7835 (mmtt) REVERT: D 88 MET cc_start: 0.7854 (ptp) cc_final: 0.7454 (ptt) REVERT: D 179 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7661 (ttm170) REVERT: D 241 GLU cc_start: 0.7583 (tt0) cc_final: 0.7201 (mp0) REVERT: D 345 ASP cc_start: 0.8375 (m-30) cc_final: 0.8034 (m-30) outliers start: 33 outliers final: 18 residues processed: 239 average time/residue: 0.7206 time to fit residues: 185.7957 Evaluate side-chains 232 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 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 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: 5.9990 chunk 49 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.159190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131556 restraints weight = 13831.083| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.21 r_work: 0.3050 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14624 Z= 0.226 Angle : 0.792 20.781 19785 Z= 0.407 Chirality : 0.051 0.468 2235 Planarity : 0.006 0.049 2380 Dihedral : 7.295 59.389 2425 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.27 % Allowed : 12.53 % 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 aren not related in a simple way. whole: 1.66 (0.20), residues: 1640 helix: 2.47 (0.22), residues: 530 sheet: 1.27 (0.24), residues: 440 loop : -0.12 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 270 TYR 0.015 0.002 TYR A 362 PHE 0.020 0.002 PHE B 356 TRP 0.011 0.002 TRP C 230 HIS 0.007 0.002 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00422 (14610) covalent geometry : angle 0.69335 (19745) SS BOND : bond 0.01211 ( 4) SS BOND : angle 1.82264 ( 10) hydrogen bonds : bond 0.10038 ( 670) hydrogen bonds : angle 4.52106 ( 2100) link_NAG-ASN : bond 0.01573 ( 10) link_NAG-ASN : angle 9.78691 ( 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 245 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7973 (ptp) cc_final: 0.7621 (ptt) REVERT: A 134 SER cc_start: 0.8181 (p) cc_final: 0.7782 (t) REVERT: A 227 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7671 (tmt) REVERT: A 457 LYS cc_start: 0.8392 (mmtp) cc_final: 0.7966 (mmtt) REVERT: E 88 MET cc_start: 0.7998 (ptp) cc_final: 0.7611 (ptt) REVERT: E 179 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7636 (ttm170) REVERT: E 227 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7420 (tmt) REVERT: E 345 ASP cc_start: 0.8592 (m-30) cc_final: 0.7852 (m-30) REVERT: B 134 SER cc_start: 0.8227 (p) cc_final: 0.7785 (t) REVERT: B 238 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8417 (mptp) REVERT: B 241 GLU cc_start: 0.7672 (tt0) cc_final: 0.7232 (mp0) REVERT: C 88 MET cc_start: 0.7971 (ptp) cc_final: 0.7704 (ptt) REVERT: C 134 SER cc_start: 0.8332 (p) cc_final: 0.7920 (t) REVERT: C 179 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7887 (ttm170) REVERT: C 227 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7277 (tmt) REVERT: C 457 LYS cc_start: 0.8409 (mtmt) cc_final: 0.7970 (mmtt) REVERT: D 88 MET cc_start: 0.7954 (ptp) cc_final: 0.7672 (ptt) REVERT: D 179 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7761 (ttm170) REVERT: D 345 ASP cc_start: 0.8634 (m-30) cc_final: 0.7871 (m-30) outliers start: 35 outliers final: 19 residues processed: 233 average time/residue: 0.7602 time to fit residues: 190.8713 Evaluate side-chains 228 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 335 MET 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 194 VAL Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 MET 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 197 MET 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: 0.8980 chunk 110 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN D 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.164125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.136644 restraints weight = 14101.332| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.24 r_work: 0.3125 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14624 Z= 0.162 Angle : 0.677 20.161 19785 Z= 0.339 Chirality : 0.047 0.479 2235 Planarity : 0.005 0.049 2380 Dihedral : 6.647 51.176 2425 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.95 % Allowed : 12.79 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.20), residues: 1640 helix: 2.68 (0.22), residues: 530 sheet: 1.13 (0.24), residues: 455 loop : -0.03 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 270 TYR 0.014 0.002 TYR D 340 PHE 0.017 0.002 PHE B 356 TRP 0.013 0.002 TRP A 349 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00270 (14610) covalent geometry : angle 0.56483 (19745) SS BOND : bond 0.00702 ( 4) SS BOND : angle 1.10448 ( 10) hydrogen bonds : bond 0.07684 ( 670) hydrogen bonds : angle 4.25835 ( 2100) link_NAG-ASN : bond 0.01712 ( 10) link_NAG-ASN : angle 9.57720 ( 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 231 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.7945 (ptp) cc_final: 0.7585 (OUTLIER) REVERT: A 227 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7620 (tmt) REVERT: A 345 ASP cc_start: 0.8500 (m-30) cc_final: 0.8042 (m-30) REVERT: E 88 MET cc_start: 0.8023 (ptp) cc_final: 0.7626 (ptt) REVERT: E 179 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7604 (ttm170) REVERT: E 227 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7391 (tmt) REVERT: E 345 ASP cc_start: 0.8405 (m-30) cc_final: 0.8035 (m-30) REVERT: B 134 SER cc_start: 0.8158 (p) cc_final: 0.7774 (t) REVERT: B 241 GLU cc_start: 0.7660 (tt0) cc_final: 0.7225 (mp0) REVERT: B 345 ASP cc_start: 0.8479 (m-30) cc_final: 0.8086 (m-30) REVERT: C 88 MET cc_start: 0.7957 (ptp) cc_final: 0.7666 (ptt) REVERT: C 179 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7854 (ttm170) REVERT: C 227 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7597 (tmt) REVERT: C 324 MET cc_start: 0.9048 (tpt) cc_final: 0.8835 (tpp) REVERT: C 345 ASP cc_start: 0.8448 (m-30) cc_final: 0.7812 (m-30) REVERT: C 457 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7841 (mmtt) REVERT: D 88 MET cc_start: 0.7923 (ptp) cc_final: 0.7495 (ptt) REVERT: D 179 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7675 (ttm170) REVERT: D 238 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8319 (mptp) REVERT: D 241 GLU cc_start: 0.7525 (tt0) cc_final: 0.7177 (mp0) REVERT: D 345 ASP cc_start: 0.8416 (m-30) cc_final: 0.7904 (m-30) outliers start: 30 outliers final: 18 residues processed: 221 average time/residue: 0.7142 time to fit residues: 170.7170 Evaluate side-chains 221 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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 256 THR Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 MET 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 238 LYS 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: 0.7980 chunk 115 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 107 optimal weight: 0.0770 chunk 142 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.164584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.137182 restraints weight = 14013.290| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.24 r_work: 0.3143 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14624 Z= 0.159 Angle : 0.671 20.411 19785 Z= 0.335 Chirality : 0.047 0.498 2235 Planarity : 0.005 0.048 2380 Dihedral : 6.451 50.800 2425 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.08 % Allowed : 12.53 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.20), residues: 1640 helix: 2.80 (0.22), residues: 530 sheet: 1.32 (0.25), residues: 430 loop : 0.04 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 270 TYR 0.014 0.002 TYR D 340 PHE 0.017 0.002 PHE B 356 TRP 0.013 0.001 TRP A 349 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00264 (14610) covalent geometry : angle 0.55795 (19745) SS BOND : bond 0.00680 ( 4) SS BOND : angle 1.29757 ( 10) hydrogen bonds : bond 0.07569 ( 670) hydrogen bonds : angle 4.21060 ( 2100) link_NAG-ASN : bond 0.01735 ( 10) link_NAG-ASN : angle 9.58740 ( 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 232 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7950 (ptp) cc_final: 0.7590 (OUTLIER) REVERT: A 227 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7616 (tmt) REVERT: A 345 ASP cc_start: 0.8469 (m-30) cc_final: 0.8062 (m-30) REVERT: E 88 MET cc_start: 0.8027 (ptp) cc_final: 0.7635 (ptt) REVERT: E 179 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7604 (ttm170) REVERT: E 227 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7414 (tmt) REVERT: E 345 ASP cc_start: 0.8389 (m-30) cc_final: 0.8075 (m-30) REVERT: B 241 GLU cc_start: 0.7663 (tt0) cc_final: 0.7216 (mp0) REVERT: B 345 ASP cc_start: 0.8466 (m-30) cc_final: 0.8134 (m-30) REVERT: C 88 MET cc_start: 0.7950 (ptp) cc_final: 0.7665 (ptt) REVERT: C 179 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7686 (ttm170) REVERT: C 227 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7582 (tmt) REVERT: C 238 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8307 (mptp) REVERT: C 345 ASP cc_start: 0.8411 (m-30) cc_final: 0.7944 (m-30) REVERT: C 457 LYS cc_start: 0.8275 (mtmt) cc_final: 0.7825 (mmtt) REVERT: D 88 MET cc_start: 0.7887 (ptp) cc_final: 0.7512 (ptt) REVERT: D 179 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7661 (ttm170) REVERT: D 345 ASP cc_start: 0.8379 (m-30) cc_final: 0.7969 (m-30) outliers start: 32 outliers final: 19 residues processed: 219 average time/residue: 0.7437 time to fit residues: 175.7744 Evaluate side-chains 222 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 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 256 THR Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 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: 2.9990 chunk 154 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.164324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.137113 restraints weight = 13833.720| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.23 r_work: 0.3083 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14624 Z= 0.198 Angle : 0.744 20.589 19785 Z= 0.378 Chirality : 0.049 0.501 2235 Planarity : 0.005 0.048 2380 Dihedral : 6.864 56.077 2425 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.82 % Allowed : 12.92 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.20), residues: 1640 helix: 2.61 (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 0.003 0.000 ARG A 270 TYR 0.015 0.002 TYR A 362 PHE 0.019 0.002 PHE B 356 TRP 0.011 0.002 TRP A 230 HIS 0.006 0.002 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00354 (14610) covalent geometry : angle 0.64212 (19745) SS BOND : bond 0.01167 ( 4) SS BOND : angle 1.38907 ( 10) hydrogen bonds : bond 0.09104 ( 670) hydrogen bonds : angle 4.39001 ( 2100) link_NAG-ASN : bond 0.01694 ( 10) link_NAG-ASN : angle 9.63875 ( 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 224 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7974 (ptp) cc_final: 0.7611 (OUTLIER) REVERT: A 227 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7622 (tmt) REVERT: A 345 ASP cc_start: 0.8598 (m-30) cc_final: 0.7997 (m-30) REVERT: E 88 MET cc_start: 0.8040 (ptp) cc_final: 0.7643 (ptt) REVERT: E 179 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7641 (ttm170) REVERT: E 227 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7407 (tmt) REVERT: E 345 ASP cc_start: 0.8568 (m-30) cc_final: 0.8078 (m-30) REVERT: B 134 SER cc_start: 0.8183 (p) cc_final: 0.7759 (t) REVERT: B 241 GLU cc_start: 0.7672 (tt0) cc_final: 0.7216 (mp0) REVERT: B 345 ASP cc_start: 0.8634 (m-30) cc_final: 0.8031 (m-30) REVERT: C 88 MET cc_start: 0.7973 (ptp) cc_final: 0.7692 (ptt) REVERT: C 134 SER cc_start: 0.8284 (p) cc_final: 0.7878 (t) REVERT: C 179 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7859 (ttm170) REVERT: C 227 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7587 (tmt) REVERT: C 238 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8312 (mptp) REVERT: C 241 GLU cc_start: 0.7632 (tt0) cc_final: 0.7284 (mp0) REVERT: C 457 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7902 (mmtt) REVERT: D 88 MET cc_start: 0.7958 (ptp) cc_final: 0.7661 (ptt) REVERT: D 179 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7713 (ttm170) REVERT: D 241 GLU cc_start: 0.7567 (tt0) cc_final: 0.7214 (mp0) outliers start: 28 outliers final: 20 residues processed: 216 average time/residue: 0.7677 time to fit residues: 178.9700 Evaluate side-chains 222 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 335 MET 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 194 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 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: 6.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 138 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.167291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140337 restraints weight = 13983.711| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.23 r_work: 0.3498 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14624 Z= 0.140 Angle : 0.638 20.181 19785 Z= 0.314 Chirality : 0.046 0.498 2235 Planarity : 0.005 0.048 2380 Dihedral : 6.221 59.523 2425 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.30 % Allowed : 13.38 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.20), residues: 1640 helix: 2.80 (0.22), residues: 535 sheet: 0.98 (0.24), residues: 465 loop : 0.11 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 191 TYR 0.015 0.002 TYR C 340 PHE 0.016 0.001 PHE A 356 TRP 0.014 0.001 TRP A 349 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00227 (14610) covalent geometry : angle 0.52069 (19745) SS BOND : bond 0.00739 ( 4) SS BOND : angle 0.88364 ( 10) hydrogen bonds : bond 0.06606 ( 670) hydrogen bonds : angle 4.10581 ( 2100) link_NAG-ASN : bond 0.01767 ( 10) link_NAG-ASN : angle 9.47442 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5842.89 seconds wall clock time: 100 minutes 6.09 seconds (6006.09 seconds total)