Starting phenix.real_space_refine on Sun Jul 5 08:27:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bu2_44899/07_2026/9bu2_44899.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bu2_44899/07_2026/9bu2_44899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bu2_44899/07_2026/9bu2_44899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bu2_44899/07_2026/9bu2_44899.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bu2_44899/07_2026/9bu2_44899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bu2_44899/07_2026/9bu2_44899.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14687 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9705 2.51 5 N 2320 2.21 5 O 2670 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14795 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "B" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "C" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "D" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "E" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 103 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 103 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 103 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 103 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 103 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PX4:plan-1': 4, 'PIO:plan-2': 5} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.29, per 1000 atoms: 0.22 Number of scatterers: 14795 At special positions: 0 Unit cell: (99.19, 100.1, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2670 8.00 N 2320 7.00 C 9705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.04 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.04 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.04 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.04 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 209 " 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 Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN A 38 " " NAG G 1 " - " ASN B 38 " " NAG H 1 " - " ASN C 38 " " NAG I 1 " - " ASN D 38 " " NAG J 1 " - " ASN E 38 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 817.4 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 25 sheets defined 39.2% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 removed outlier: 4.373A pdb=" N PHE A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 86 through 93 removed outlier: 4.536A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 92 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 removed outlier: 3.544A pdb=" N ILE A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.579A pdb=" N SER A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 248 through 270 Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.975A pdb=" N ARG A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 421 removed outlier: 3.768A pdb=" N ARG A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'B' and resid 9 through 19 removed outlier: 4.372A pdb=" N PHE B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 86 through 93 removed outlier: 4.536A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 92 " --> pdb=" O MET B 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 93 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 removed outlier: 3.544A pdb=" N ILE B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.579A pdb=" N SER B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 248 through 270 Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.974A pdb=" N ARG B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 421 removed outlier: 3.768A pdb=" N ARG B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'C' and resid 9 through 19 removed outlier: 4.372A pdb=" N PHE C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 86 through 93 removed outlier: 4.536A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 92 " --> pdb=" O MET C 89 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 removed outlier: 3.544A pdb=" N ILE C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 241 removed outlier: 3.579A pdb=" N SER C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 248 through 270 Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.974A pdb=" N ARG C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 421 removed outlier: 3.768A pdb=" N ARG C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C 392 " --> pdb=" O PHE C 388 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA C 401 " --> pdb=" O THR C 397 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'D' and resid 9 through 19 removed outlier: 4.373A pdb=" N PHE D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 86 through 93 removed outlier: 4.536A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 92 " --> pdb=" O MET D 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 227 removed outlier: 3.544A pdb=" N ILE D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.579A pdb=" N SER D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 248 through 270 Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.974A pdb=" N ARG D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 421 removed outlier: 3.769A pdb=" N ARG D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA D 401 " --> pdb=" O THR D 397 " (cutoff:3.500A) Proline residue: D 404 - end of helix Processing helix chain 'E' and resid 9 through 19 removed outlier: 4.373A pdb=" N PHE E 13 " --> pdb=" O SER E 9 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU E 14 " --> pdb=" O PRO E 10 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 86 through 93 removed outlier: 4.537A pdb=" N ASP E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER E 92 " --> pdb=" O MET E 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 93 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 227 removed outlier: 3.544A pdb=" N ILE E 225 " --> pdb=" O GLY E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 241 removed outlier: 3.579A pdb=" N SER E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 244 No H-bonds generated for 'chain 'E' and resid 242 through 244' Processing helix chain 'E' and resid 248 through 270 Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.975A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 421 removed outlier: 3.768A pdb=" N ARG E 391 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA E 392 " --> pdb=" O PHE E 388 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) Proline residue: E 404 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.609A pdb=" N LEU A 83 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 120 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP A 68 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 6.683A pdb=" N THR A 135 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA A 106 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR A 133 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP A 68 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.570A pdb=" N ARG A 196 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA6, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.609A pdb=" N LEU B 83 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 120 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP B 68 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 107 removed outlier: 6.683A pdb=" N THR B 135 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA B 106 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR B 133 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP B 68 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.570A pdb=" N ARG B 196 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 200 through 201 Processing sheet with id=AB2, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.609A pdb=" N LEU C 83 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 120 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP C 68 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 107 removed outlier: 6.683A pdb=" N THR C 135 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA C 106 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR C 133 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP C 68 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 98 through 100 Processing sheet with id=AB5, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.570A pdb=" N ARG C 196 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 201 Processing sheet with id=AB7, first strand: chain 'D' and resid 82 through 84 removed outlier: 3.609A pdb=" N LEU D 83 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 120 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP D 68 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 107 removed outlier: 6.683A pdb=" N THR D 135 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA D 106 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR D 133 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP D 68 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 98 through 100 Processing sheet with id=AC1, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.570A pdb=" N ARG D 196 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 200 through 201 Processing sheet with id=AC3, first strand: chain 'E' and resid 82 through 84 removed outlier: 3.609A pdb=" N LEU E 83 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 120 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP E 68 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 103 through 107 removed outlier: 6.682A pdb=" N THR E 135 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA E 106 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR E 133 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP E 68 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 98 through 100 Processing sheet with id=AC6, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.569A pdb=" N ARG E 196 " --> pdb=" O GLU E 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 200 through 201 805 hydrogen bonds defined for protein. 2340 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: 2.43 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2290 1.32 - 1.44: 4161 1.44 - 1.57: 8254 1.57 - 1.69: 235 1.69 - 1.82: 165 Bond restraints: 15105 Sorted by residual: bond pdb=" C23 PX4 C 508 " pdb=" O7 PX4 C 508 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" C23 PX4 D 508 " pdb=" O7 PX4 D 508 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" C23 PX4 A 508 " pdb=" O7 PX4 A 508 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" C23 PX4 A 509 " pdb=" O7 PX4 A 509 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C23 PX4 E 502 " pdb=" O7 PX4 E 502 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.68e+01 ... (remaining 15100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 19343 1.71 - 3.42: 669 3.42 - 5.14: 238 5.14 - 6.85: 45 6.85 - 8.56: 25 Bond angle restraints: 20320 Sorted by residual: angle pdb=" C PRO D 175 " pdb=" CA PRO D 175 " pdb=" CB PRO D 175 " ideal model delta sigma weight residual 112.55 106.48 6.07 1.50e+00 4.44e-01 1.64e+01 angle pdb=" C PRO C 175 " pdb=" CA PRO C 175 " pdb=" CB PRO C 175 " ideal model delta sigma weight residual 112.55 106.49 6.06 1.50e+00 4.44e-01 1.63e+01 angle pdb=" C PRO A 175 " pdb=" CA PRO A 175 " pdb=" CB PRO A 175 " ideal model delta sigma weight residual 112.55 106.51 6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" C PRO E 175 " pdb=" CA PRO E 175 " pdb=" CB PRO E 175 " ideal model delta sigma weight residual 112.55 106.52 6.03 1.50e+00 4.44e-01 1.62e+01 angle pdb=" C PRO B 175 " pdb=" CA PRO B 175 " pdb=" CB PRO B 175 " ideal model delta sigma weight residual 112.55 106.53 6.02 1.50e+00 4.44e-01 1.61e+01 ... (remaining 20315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 8283 17.06 - 34.12: 742 34.12 - 51.18: 90 51.18 - 68.24: 40 68.24 - 85.29: 30 Dihedral angle restraints: 9185 sinusoidal: 4050 harmonic: 5135 Sorted by residual: dihedral pdb=" CB CYS E 198 " pdb=" SG CYS E 198 " pdb=" SG CYS E 209 " pdb=" CB CYS E 209 " ideal model delta sinusoidal sigma weight residual -86.00 -9.36 -76.64 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS D 198 " pdb=" SG CYS D 198 " pdb=" SG CYS D 209 " pdb=" CB CYS D 209 " ideal model delta sinusoidal sigma weight residual -86.00 -9.38 -76.62 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS B 198 " pdb=" SG CYS B 198 " pdb=" SG CYS B 209 " pdb=" CB CYS B 209 " ideal model delta sinusoidal sigma weight residual -86.00 -9.38 -76.62 1 1.00e+01 1.00e-02 7.38e+01 ... (remaining 9182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1396 0.033 - 0.066: 534 0.066 - 0.099: 182 0.099 - 0.133: 114 0.133 - 0.166: 19 Chirality restraints: 2245 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN E 38 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 38 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 38 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 2242 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 86 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 87 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 86 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO E 87 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 87 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 87 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 86 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO A 87 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " -0.022 5.00e-02 4.00e+02 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4094 2.82 - 3.34: 12607 3.34 - 3.86: 22352 3.86 - 4.38: 25825 4.38 - 4.90: 46922 Nonbonded interactions: 111800 Sorted by model distance: nonbonded pdb=" OE1 GLU E 169 " pdb=" OH TYR E 197 " model vdw 2.303 3.040 nonbonded pdb=" OE1 GLU D 169 " pdb=" OH TYR D 197 " model vdw 2.303 3.040 nonbonded pdb=" OE1 GLU C 169 " pdb=" OH TYR C 197 " model vdw 2.303 3.040 nonbonded pdb=" OE1 GLU A 169 " pdb=" OH TYR A 197 " model vdw 2.303 3.040 nonbonded pdb=" OE1 GLU B 169 " pdb=" OH TYR B 197 " model vdw 2.304 3.040 ... (remaining 111795 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 8 through 427 or (resid 506 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)))) selection = (chain 'B' and (resid 8 through 427 or (resid 505 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)))) selection = (chain 'C' and (resid 8 through 427 or (resid 505 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)))) selection = (chain 'D' and (resid 8 through 427 or (resid 505 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)))) selection = (chain 'E' and (resid 8 through 427 or resid 504)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.000 Find NCS groups from input model: 0.420 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 : 0.012 0.137 15120 Z= 0.612 Angle : 0.890 8.562 20360 Z= 0.430 Chirality : 0.046 0.166 2245 Planarity : 0.004 0.040 2520 Dihedral : 13.650 85.294 5830 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1710 helix: 2.05 (0.22), residues: 555 sheet: 0.04 (0.25), residues: 420 loop : -0.91 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 309 TYR 0.016 0.002 TYR E 301 PHE 0.012 0.001 PHE B 99 TRP 0.007 0.001 TRP E 415 HIS 0.002 0.001 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.01212 / 0.61 (15105) covalent geometry : angle 0.88531 / 0.43 (20320) SS BOND : bond 0.00574 / 0.29 ( 5) SS BOND : angle 4.19843 / 2.21 ( 10) hydrogen bonds : bond 0.19021 / 12.44 ( 665) hydrogen bonds : angle 6.28930 / 4.20 ( 2340) link_BETA1-4 : bond 0.00333 / 0.17 ( 5) link_BETA1-4 : angle 1.14354 / 0.67 ( 15) link_NAG-ASN : bond 0.00119 / 0.06 ( 5) link_NAG-ASN : angle 0.42845 / 0.26 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.500 Fit side-chains REVERT: A 173 GLU cc_start: 0.7723 (pm20) cc_final: 0.7479 (pm20) REVERT: A 191 GLU cc_start: 0.8064 (pm20) cc_final: 0.7750 (pm20) REVERT: B 203 ASN cc_start: 0.8587 (m-40) cc_final: 0.8249 (m-40) REVERT: B 246 MET cc_start: 0.8296 (ptp) cc_final: 0.7997 (ptp) REVERT: C 18 MET cc_start: 0.8696 (ptp) cc_final: 0.8445 (ptp) REVERT: C 203 ASN cc_start: 0.8606 (m-40) cc_final: 0.8252 (m-40) REVERT: C 211 GLU cc_start: 0.8846 (tt0) cc_final: 0.8368 (tt0) REVERT: C 246 MET cc_start: 0.8303 (ptp) cc_final: 0.8097 (ptp) REVERT: C 421 LEU cc_start: 0.7138 (tt) cc_final: 0.6904 (tt) REVERT: D 113 THR cc_start: 0.8971 (p) cc_final: 0.8550 (p) REVERT: D 191 GLU cc_start: 0.8016 (pm20) cc_final: 0.7742 (pm20) REVERT: D 203 ASN cc_start: 0.8559 (m-40) cc_final: 0.8338 (m-40) REVERT: E 173 GLU cc_start: 0.7837 (pm20) cc_final: 0.7569 (pm20) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.5628 time to fit residues: 225.6444 Evaluate side-chains 319 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 ASN A 226 GLN B 203 ASN B 226 GLN C 144 ASN C 203 ASN C 226 GLN C 266 GLN D 144 ASN D 150 GLN D 186 GLN D 203 ASN D 226 GLN E 226 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098570 restraints weight = 21543.888| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.03 r_work: 0.3019 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15120 Z= 0.129 Angle : 0.581 7.557 20360 Z= 0.299 Chirality : 0.044 0.173 2245 Planarity : 0.004 0.030 2520 Dihedral : 9.620 59.117 2430 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.36 % Allowed : 9.68 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1710 helix: 2.42 (0.22), residues: 550 sheet: 0.36 (0.25), residues: 430 loop : -0.75 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 309 TYR 0.013 0.001 TYR C 301 PHE 0.019 0.001 PHE B 13 TRP 0.004 0.001 TRP A 68 HIS 0.001 0.000 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (15105) covalent geometry : angle 0.57660 / 0.30 (20320) SS BOND : bond 0.00211 / 0.11 ( 5) SS BOND : angle 2.92237 / 1.52 ( 10) hydrogen bonds : bond 0.05162 / 3.53 ( 665) hydrogen bonds : angle 4.37083 / 2.95 ( 2340) link_BETA1-4 : bond 0.00349 / 0.18 ( 5) link_BETA1-4 : angle 1.14403 / 0.68 ( 15) link_NAG-ASN : bond 0.00217 / 0.11 ( 5) link_NAG-ASN : angle 0.33852 / 0.20 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 344 time to evaluate : 0.585 Fit side-chains REVERT: A 18 MET cc_start: 0.8483 (ptp) cc_final: 0.8281 (ptp) REVERT: A 173 GLU cc_start: 0.7691 (pm20) cc_final: 0.7419 (pm20) REVERT: A 191 GLU cc_start: 0.8538 (pm20) cc_final: 0.8167 (pm20) REVERT: A 217 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8204 (mp0) REVERT: B 173 GLU cc_start: 0.7602 (pm20) cc_final: 0.7307 (pm20) REVERT: B 203 ASN cc_start: 0.8649 (m110) cc_final: 0.8344 (m110) REVERT: B 246 MET cc_start: 0.8168 (ptp) cc_final: 0.7920 (ptp) REVERT: B 309 ARG cc_start: 0.7284 (pmm-80) cc_final: 0.7063 (pmm-80) REVERT: C 89 MET cc_start: 0.8312 (ppp) cc_final: 0.7548 (pp-130) REVERT: C 203 ASN cc_start: 0.8653 (m110) cc_final: 0.8357 (m-40) REVERT: D 173 GLU cc_start: 0.7449 (pm20) cc_final: 0.7079 (pm20) REVERT: E 173 GLU cc_start: 0.7800 (pm20) cc_final: 0.7486 (pm20) REVERT: E 217 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8489 (mt-10) REVERT: E 239 TRP cc_start: 0.8174 (m-10) cc_final: 0.7761 (m-10) outliers start: 37 outliers final: 19 residues processed: 349 average time/residue: 0.5592 time to fit residues: 215.8640 Evaluate side-chains 342 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 323 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 33 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 95 optimal weight: 0.0050 chunk 141 optimal weight: 1.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN B 226 GLN C 226 GLN D 186 GLN E 186 GLN E 226 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.093792 restraints weight = 21958.026| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.07 r_work: 0.2941 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15120 Z= 0.219 Angle : 0.640 7.584 20360 Z= 0.326 Chirality : 0.046 0.198 2245 Planarity : 0.004 0.040 2520 Dihedral : 9.166 59.854 2430 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 4.46 % Allowed : 13.25 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.20), residues: 1710 helix: 2.11 (0.21), residues: 585 sheet: 0.37 (0.25), residues: 400 loop : -1.14 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 131 TYR 0.022 0.002 TYR E 418 PHE 0.014 0.002 PHE E 99 TRP 0.007 0.001 TRP A 68 HIS 0.004 0.001 HIS E 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (15105) covalent geometry : angle 0.63786 / 0.33 (20320) SS BOND : bond 0.00430 / 0.22 ( 5) SS BOND : angle 2.19814 / 1.13 ( 10) hydrogen bonds : bond 0.06148 / 4.19 ( 665) hydrogen bonds : angle 4.44011 / 3.02 ( 2340) link_BETA1-4 : bond 0.00327 / 0.17 ( 5) link_BETA1-4 : angle 1.20778 / 0.73 ( 15) link_NAG-ASN : bond 0.00110 / 0.06 ( 5) link_NAG-ASN : angle 0.66790 / 0.40 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 327 time to evaluate : 0.587 Fit side-chains REVERT: A 173 GLU cc_start: 0.7866 (pm20) cc_final: 0.7564 (pm20) REVERT: B 173 GLU cc_start: 0.7802 (pm20) cc_final: 0.7439 (pm20) REVERT: B 203 ASN cc_start: 0.8683 (m110) cc_final: 0.8354 (m-40) REVERT: B 211 GLU cc_start: 0.9149 (tt0) cc_final: 0.8876 (tt0) REVERT: B 219 GLN cc_start: 0.8760 (mm110) cc_final: 0.8302 (mt0) REVERT: B 246 MET cc_start: 0.8272 (ptp) cc_final: 0.8057 (ptp) REVERT: C 203 ASN cc_start: 0.8691 (m110) cc_final: 0.8366 (m-40) REVERT: C 211 GLU cc_start: 0.9197 (tt0) cc_final: 0.8772 (tt0) REVERT: C 213 ARG cc_start: 0.8674 (mtt-85) cc_final: 0.8366 (mtt-85) REVERT: D 173 GLU cc_start: 0.7554 (pm20) cc_final: 0.7157 (pm20) REVERT: E 173 GLU cc_start: 0.7881 (pm20) cc_final: 0.7565 (pm20) REVERT: E 219 GLN cc_start: 0.8836 (mm110) cc_final: 0.8530 (mt0) outliers start: 70 outliers final: 41 residues processed: 346 average time/residue: 0.5734 time to fit residues: 218.7551 Evaluate side-chains 368 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 327 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 402 CYS Chi-restraints excluded: chain E residue 409 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 102 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 108 optimal weight: 0.0040 chunk 46 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 ASN A 226 GLN B 226 GLN C 226 GLN D 144 ASN D 186 GLN D 226 GLN E 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097978 restraints weight = 21619.808| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.04 r_work: 0.3003 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15120 Z= 0.118 Angle : 0.563 9.317 20360 Z= 0.285 Chirality : 0.043 0.188 2245 Planarity : 0.004 0.041 2520 Dihedral : 8.375 56.513 2430 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.82 % Allowed : 15.10 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1710 helix: 2.48 (0.22), residues: 555 sheet: 0.49 (0.25), residues: 430 loop : -0.67 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 309 TYR 0.014 0.001 TYR E 418 PHE 0.013 0.001 PHE C 13 TRP 0.008 0.001 TRP B 415 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (15105) covalent geometry : angle 0.55968 / 0.28 (20320) SS BOND : bond 0.00578 / 0.29 ( 5) SS BOND : angle 2.61811 / 1.37 ( 10) hydrogen bonds : bond 0.04744 / 3.26 ( 665) hydrogen bonds : angle 4.07663 / 2.77 ( 2340) link_BETA1-4 : bond 0.00398 / 0.20 ( 5) link_BETA1-4 : angle 1.13922 / 0.68 ( 15) link_NAG-ASN : bond 0.00281 / 0.14 ( 5) link_NAG-ASN : angle 0.27419 / 0.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 338 time to evaluate : 0.731 Fit side-chains REVERT: A 173 GLU cc_start: 0.7909 (pm20) cc_final: 0.7616 (pm20) REVERT: A 217 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8215 (mp0) REVERT: B 173 GLU cc_start: 0.7779 (pm20) cc_final: 0.7388 (pm20) REVERT: B 203 ASN cc_start: 0.8647 (m110) cc_final: 0.8368 (m110) REVERT: C 89 MET cc_start: 0.8268 (ppp) cc_final: 0.7665 (pp-130) REVERT: C 203 ASN cc_start: 0.8668 (m110) cc_final: 0.8322 (m-40) REVERT: C 213 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8423 (mtt-85) REVERT: D 173 GLU cc_start: 0.7616 (pm20) cc_final: 0.7229 (pm20) REVERT: E 89 MET cc_start: 0.8321 (ppp) cc_final: 0.7700 (ppp) REVERT: E 173 GLU cc_start: 0.7871 (pm20) cc_final: 0.7560 (pm20) REVERT: E 300 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8532 (tm-30) outliers start: 60 outliers final: 36 residues processed: 347 average time/residue: 0.5784 time to fit residues: 221.6635 Evaluate side-chains 362 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 326 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 402 CYS Chi-restraints excluded: chain E residue 409 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 97 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 152 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 69 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN C 226 GLN D 186 GLN E 144 ASN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098179 restraints weight = 21405.971| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.08 r_work: 0.3007 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15120 Z= 0.115 Angle : 0.550 8.665 20360 Z= 0.278 Chirality : 0.043 0.187 2245 Planarity : 0.004 0.042 2520 Dihedral : 7.797 54.509 2430 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.63 % Allowed : 16.56 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.21), residues: 1710 helix: 2.49 (0.22), residues: 560 sheet: 0.57 (0.25), residues: 430 loop : -0.62 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 309 TYR 0.014 0.001 TYR B 301 PHE 0.011 0.001 PHE B 99 TRP 0.006 0.001 TRP D 415 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (15105) covalent geometry : angle 0.54705 / 0.28 (20320) SS BOND : bond 0.00176 / 0.09 ( 5) SS BOND : angle 2.36956 / 1.24 ( 10) hydrogen bonds : bond 0.04446 / 3.06 ( 665) hydrogen bonds : angle 3.97433 / 2.70 ( 2340) link_BETA1-4 : bond 0.00372 / 0.19 ( 5) link_BETA1-4 : angle 1.20166 / 0.72 ( 15) link_NAG-ASN : bond 0.00206 / 0.11 ( 5) link_NAG-ASN : angle 0.33748 / 0.20 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 330 time to evaluate : 0.581 Fit side-chains REVERT: A 173 GLU cc_start: 0.7949 (pm20) cc_final: 0.7643 (pm20) REVERT: A 217 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8284 (mp0) REVERT: B 89 MET cc_start: 0.8247 (ppp) cc_final: 0.7677 (ppp) REVERT: B 173 GLU cc_start: 0.7772 (pm20) cc_final: 0.7346 (pm20) REVERT: B 203 ASN cc_start: 0.8654 (m110) cc_final: 0.8387 (m110) REVERT: C 89 MET cc_start: 0.8337 (ppp) cc_final: 0.7774 (pp-130) REVERT: C 203 ASN cc_start: 0.8658 (m110) cc_final: 0.8337 (m-40) REVERT: C 213 ARG cc_start: 0.8649 (mtt-85) cc_final: 0.8446 (mtt-85) REVERT: C 239 TRP cc_start: 0.8128 (m-10) cc_final: 0.7586 (m-10) REVERT: D 173 GLU cc_start: 0.7700 (pm20) cc_final: 0.7306 (pm20) REVERT: D 239 TRP cc_start: 0.8049 (m-10) cc_final: 0.7675 (m-10) REVERT: E 173 GLU cc_start: 0.7903 (pm20) cc_final: 0.7558 (pm20) REVERT: E 190 LYS cc_start: 0.8434 (mmmm) cc_final: 0.8083 (mptm) REVERT: E 213 ARG cc_start: 0.8615 (mtt-85) cc_final: 0.8300 (mtt-85) REVERT: E 239 TRP cc_start: 0.8145 (m-10) cc_final: 0.7701 (m-10) outliers start: 57 outliers final: 34 residues processed: 339 average time/residue: 0.5926 time to fit residues: 221.0138 Evaluate side-chains 359 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 325 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 402 CYS Chi-restraints excluded: chain E residue 409 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 97 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 125 optimal weight: 0.0570 chunk 161 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN B 226 GLN D 46 ASN D 186 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098650 restraints weight = 21230.448| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.06 r_work: 0.3016 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15120 Z= 0.113 Angle : 0.553 9.843 20360 Z= 0.277 Chirality : 0.043 0.193 2245 Planarity : 0.003 0.043 2520 Dihedral : 7.390 58.951 2430 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 3.57 % Allowed : 17.39 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1710 helix: 2.53 (0.22), residues: 560 sheet: 0.60 (0.25), residues: 430 loop : -0.56 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 309 TYR 0.015 0.001 TYR C 301 PHE 0.011 0.001 PHE D 99 TRP 0.006 0.001 TRP D 415 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (15105) covalent geometry : angle 0.55068 / 0.28 (20320) SS BOND : bond 0.00156 / 0.08 ( 5) SS BOND : angle 2.24660 / 1.15 ( 10) hydrogen bonds : bond 0.04280 / 2.95 ( 665) hydrogen bonds : angle 3.92010 / 2.66 ( 2340) link_BETA1-4 : bond 0.00374 / 0.19 ( 5) link_BETA1-4 : angle 1.20232 / 0.72 ( 15) link_NAG-ASN : bond 0.00216 / 0.11 ( 5) link_NAG-ASN : angle 0.33596 / 0.20 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 332 time to evaluate : 0.624 Fit side-chains REVERT: A 173 GLU cc_start: 0.8001 (pm20) cc_final: 0.7685 (pm20) REVERT: A 190 LYS cc_start: 0.8434 (mmmm) cc_final: 0.8186 (mptm) REVERT: B 173 GLU cc_start: 0.7801 (pm20) cc_final: 0.7355 (pm20) REVERT: B 203 ASN cc_start: 0.8655 (m110) cc_final: 0.8415 (m110) REVERT: C 89 MET cc_start: 0.8313 (ppp) cc_final: 0.7785 (pp-130) REVERT: C 203 ASN cc_start: 0.8636 (m110) cc_final: 0.8327 (m-40) REVERT: D 173 GLU cc_start: 0.7722 (pm20) cc_final: 0.7348 (pm20) REVERT: D 239 TRP cc_start: 0.8050 (m-10) cc_final: 0.7613 (m-10) REVERT: E 173 GLU cc_start: 0.7910 (pm20) cc_final: 0.7606 (pm20) REVERT: E 190 LYS cc_start: 0.8459 (mmmm) cc_final: 0.8112 (mptm) REVERT: E 213 ARG cc_start: 0.8609 (mtt-85) cc_final: 0.8334 (mtt-85) outliers start: 56 outliers final: 38 residues processed: 345 average time/residue: 0.5907 time to fit residues: 224.5188 Evaluate side-chains 361 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 323 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 402 CYS Chi-restraints excluded: chain E residue 409 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 48 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN B 226 GLN D 186 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097524 restraints weight = 21276.833| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.03 r_work: 0.3000 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15120 Z= 0.135 Angle : 0.576 10.409 20360 Z= 0.288 Chirality : 0.044 0.196 2245 Planarity : 0.004 0.043 2520 Dihedral : 7.169 59.878 2430 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 3.25 % Allowed : 18.22 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.20), residues: 1710 helix: 2.71 (0.22), residues: 530 sheet: 0.56 (0.25), residues: 430 loop : -0.66 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 213 TYR 0.017 0.001 TYR E 418 PHE 0.012 0.001 PHE D 99 TRP 0.006 0.001 TRP B 415 HIS 0.002 0.001 HIS E 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (15105) covalent geometry : angle 0.57372 / 0.29 (20320) SS BOND : bond 0.00353 / 0.19 ( 5) SS BOND : angle 2.15564 / 1.10 ( 10) hydrogen bonds : bond 0.04549 / 3.14 ( 665) hydrogen bonds : angle 3.97428 / 2.71 ( 2340) link_BETA1-4 : bond 0.00341 / 0.17 ( 5) link_BETA1-4 : angle 1.20630 / 0.72 ( 15) link_NAG-ASN : bond 0.00131 / 0.07 ( 5) link_NAG-ASN : angle 0.45866 / 0.27 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 325 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.8014 (pm20) cc_final: 0.7685 (pm20) REVERT: A 190 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8246 (mptm) REVERT: B 89 MET cc_start: 0.8284 (ppp) cc_final: 0.7750 (ppp) REVERT: B 173 GLU cc_start: 0.7873 (pm20) cc_final: 0.7443 (pm20) REVERT: B 203 ASN cc_start: 0.8626 (m110) cc_final: 0.8359 (m110) REVERT: B 213 ARG cc_start: 0.8666 (mtt-85) cc_final: 0.8313 (mtt-85) REVERT: C 203 ASN cc_start: 0.8639 (m110) cc_final: 0.8328 (m-40) REVERT: D 173 GLU cc_start: 0.7791 (pm20) cc_final: 0.7416 (pm20) REVERT: E 173 GLU cc_start: 0.7933 (pm20) cc_final: 0.7654 (pm20) REVERT: E 190 LYS cc_start: 0.8508 (mmmm) cc_final: 0.8156 (mptm) REVERT: E 213 ARG cc_start: 0.8655 (mtt-85) cc_final: 0.8390 (mtt-85) REVERT: E 239 TRP cc_start: 0.8184 (m-10) cc_final: 0.7815 (m-10) outliers start: 51 outliers final: 40 residues processed: 335 average time/residue: 0.5862 time to fit residues: 215.4455 Evaluate side-chains 364 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 324 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 402 CYS Chi-restraints excluded: chain E residue 409 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 167 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 226 GLN D 186 GLN D 226 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097954 restraints weight = 21508.363| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.07 r_work: 0.3005 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15120 Z= 0.129 Angle : 0.587 10.970 20360 Z= 0.291 Chirality : 0.044 0.202 2245 Planarity : 0.003 0.044 2520 Dihedral : 6.850 59.522 2430 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.93 % Allowed : 18.66 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1710 helix: 2.73 (0.22), residues: 530 sheet: 0.57 (0.25), residues: 430 loop : -0.66 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 213 TYR 0.015 0.001 TYR E 418 PHE 0.015 0.001 PHE D 13 TRP 0.007 0.001 TRP B 415 HIS 0.001 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (15105) covalent geometry : angle 0.58522 / 0.29 (20320) SS BOND : bond 0.00133 / 0.07 ( 5) SS BOND : angle 2.00594 / 1.03 ( 10) hydrogen bonds : bond 0.04440 / 3.06 ( 665) hydrogen bonds : angle 3.96004 / 2.69 ( 2340) link_BETA1-4 : bond 0.00375 / 0.19 ( 5) link_BETA1-4 : angle 1.19539 / 0.71 ( 15) link_NAG-ASN : bond 0.00168 / 0.09 ( 5) link_NAG-ASN : angle 0.40680 / 0.23 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 323 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.8042 (pm20) cc_final: 0.7713 (pm20) REVERT: A 190 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8287 (mptm) REVERT: B 13 PHE cc_start: 0.7661 (t80) cc_final: 0.7459 (t80) REVERT: B 89 MET cc_start: 0.8255 (ppp) cc_final: 0.7708 (ppp) REVERT: B 173 GLU cc_start: 0.7908 (pm20) cc_final: 0.7476 (pm20) REVERT: B 203 ASN cc_start: 0.8624 (m110) cc_final: 0.8393 (m110) REVERT: B 211 GLU cc_start: 0.9146 (tt0) cc_final: 0.8801 (tt0) REVERT: C 203 ASN cc_start: 0.8637 (m110) cc_final: 0.8322 (m-40) REVERT: C 239 TRP cc_start: 0.8193 (m-10) cc_final: 0.7746 (m-10) REVERT: D 110 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: D 173 GLU cc_start: 0.7827 (pm20) cc_final: 0.7432 (pm20) REVERT: D 239 TRP cc_start: 0.8070 (m-10) cc_final: 0.7749 (m-10) REVERT: E 173 GLU cc_start: 0.7962 (pm20) cc_final: 0.7671 (pm20) REVERT: E 190 LYS cc_start: 0.8514 (mmmm) cc_final: 0.8167 (mptm) REVERT: E 213 ARG cc_start: 0.8646 (mtt-85) cc_final: 0.8386 (mtt-85) REVERT: E 239 TRP cc_start: 0.8184 (m-10) cc_final: 0.7765 (m-10) outliers start: 46 outliers final: 37 residues processed: 331 average time/residue: 0.5668 time to fit residues: 206.4764 Evaluate side-chains 351 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 313 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 402 CYS Chi-restraints excluded: chain E residue 409 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 84 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN A 226 GLN D 186 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098057 restraints weight = 21482.444| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.03 r_work: 0.3000 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15120 Z= 0.137 Angle : 0.595 11.849 20360 Z= 0.294 Chirality : 0.044 0.201 2245 Planarity : 0.004 0.043 2520 Dihedral : 6.670 57.178 2430 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 3.38 % Allowed : 17.90 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.20), residues: 1710 helix: 2.67 (0.22), residues: 535 sheet: 0.64 (0.25), residues: 420 loop : -0.71 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 213 TYR 0.016 0.001 TYR C 301 PHE 0.013 0.001 PHE D 13 TRP 0.006 0.001 TRP B 415 HIS 0.002 0.001 HIS A 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (15105) covalent geometry : angle 0.59273 / 0.29 (20320) SS BOND : bond 0.00180 / 0.09 ( 5) SS BOND : angle 1.91704 / 0.98 ( 10) hydrogen bonds : bond 0.04521 / 3.11 ( 665) hydrogen bonds : angle 3.98301 / 2.71 ( 2340) link_BETA1-4 : bond 0.00398 / 0.20 ( 5) link_BETA1-4 : angle 1.21249 / 0.73 ( 15) link_NAG-ASN : bond 0.00133 / 0.07 ( 5) link_NAG-ASN : angle 0.46630 / 0.27 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 322 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.8057 (pm20) cc_final: 0.7722 (pm20) REVERT: A 190 LYS cc_start: 0.8545 (mmmm) cc_final: 0.8310 (mptm) REVERT: B 89 MET cc_start: 0.8239 (ppp) cc_final: 0.7684 (ppp) REVERT: B 173 GLU cc_start: 0.7928 (pm20) cc_final: 0.7501 (pm20) REVERT: B 203 ASN cc_start: 0.8636 (m110) cc_final: 0.8402 (m110) REVERT: B 211 GLU cc_start: 0.9151 (tt0) cc_final: 0.8773 (tt0) REVERT: C 132 LEU cc_start: 0.8899 (mp) cc_final: 0.8692 (mp) REVERT: C 203 ASN cc_start: 0.8638 (m110) cc_final: 0.8321 (m-40) REVERT: D 89 MET cc_start: 0.8375 (ppp) cc_final: 0.8056 (ppp) REVERT: D 110 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: D 173 GLU cc_start: 0.7793 (pm20) cc_final: 0.7406 (pm20) REVERT: E 173 GLU cc_start: 0.8069 (pm20) cc_final: 0.7741 (pm20) REVERT: E 190 LYS cc_start: 0.8522 (mmmm) cc_final: 0.8195 (mptm) REVERT: E 213 ARG cc_start: 0.8640 (mtt-85) cc_final: 0.8377 (mtt-85) REVERT: E 239 TRP cc_start: 0.8193 (m-10) cc_final: 0.7818 (m-10) outliers start: 53 outliers final: 42 residues processed: 333 average time/residue: 0.5769 time to fit residues: 211.5514 Evaluate side-chains 363 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 320 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 402 CYS Chi-restraints excluded: chain E residue 409 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 24 optimal weight: 0.7980 chunk 90 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 130 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN A 226 GLN B 226 GLN D 186 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099158 restraints weight = 21416.286| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.07 r_work: 0.3023 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15120 Z= 0.113 Angle : 0.592 11.029 20360 Z= 0.292 Chirality : 0.044 0.202 2245 Planarity : 0.003 0.038 2520 Dihedral : 6.343 59.621 2430 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.61 % Allowed : 19.04 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1710 helix: 2.72 (0.23), residues: 535 sheet: 0.62 (0.25), residues: 430 loop : -0.60 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 309 TYR 0.015 0.001 TYR E 301 PHE 0.014 0.001 PHE D 13 TRP 0.006 0.001 TRP E 415 HIS 0.002 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (15105) covalent geometry : angle 0.58965 / 0.29 (20320) SS BOND : bond 0.00071 / 0.04 ( 5) SS BOND : angle 2.34071 / 1.26 ( 10) hydrogen bonds : bond 0.04123 / 2.84 ( 665) hydrogen bonds : angle 3.87987 / 2.64 ( 2340) link_BETA1-4 : bond 0.00297 / 0.15 ( 5) link_BETA1-4 : angle 1.17130 / 0.70 ( 15) link_NAG-ASN : bond 0.00224 / 0.11 ( 5) link_NAG-ASN : angle 0.31525 / 0.18 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 324 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.8024 (pm20) cc_final: 0.7727 (pm20) REVERT: A 190 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8314 (mptm) REVERT: B 89 MET cc_start: 0.8250 (ppp) cc_final: 0.7697 (ppp) REVERT: B 173 GLU cc_start: 0.7900 (pm20) cc_final: 0.7480 (pm20) REVERT: B 203 ASN cc_start: 0.8628 (m110) cc_final: 0.8381 (m110) REVERT: B 211 GLU cc_start: 0.9145 (tt0) cc_final: 0.8783 (tt0) REVERT: C 132 LEU cc_start: 0.8867 (mp) cc_final: 0.8634 (mp) REVERT: C 203 ASN cc_start: 0.8621 (m110) cc_final: 0.8357 (m-40) REVERT: D 89 MET cc_start: 0.8366 (ppp) cc_final: 0.8036 (pp-130) REVERT: D 110 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: D 173 GLU cc_start: 0.7788 (pm20) cc_final: 0.7466 (pm20) REVERT: E 89 MET cc_start: 0.8387 (ppp) cc_final: 0.7810 (pp-130) REVERT: E 173 GLU cc_start: 0.8065 (pm20) cc_final: 0.7784 (pm20) REVERT: E 190 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8207 (mptm) REVERT: E 213 ARG cc_start: 0.8635 (mtt-85) cc_final: 0.8372 (mtt-85) REVERT: E 217 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8668 (mt-10) outliers start: 41 outliers final: 34 residues processed: 333 average time/residue: 0.5655 time to fit residues: 207.7593 Evaluate side-chains 349 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 314 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 167 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 85 optimal weight: 0.0020 chunk 119 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.7088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN A 226 GLN B 46 ASN B 115 ASN B 226 GLN D 186 GLN E 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099349 restraints weight = 21359.485| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.07 r_work: 0.3025 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15120 Z= 0.115 Angle : 0.598 12.951 20360 Z= 0.293 Chirality : 0.044 0.198 2245 Planarity : 0.003 0.029 2520 Dihedral : 6.074 59.491 2430 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.80 % Allowed : 19.04 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.21), residues: 1710 helix: 2.76 (0.23), residues: 535 sheet: 0.65 (0.25), residues: 430 loop : -0.59 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 213 TYR 0.015 0.001 TYR E 301 PHE 0.013 0.001 PHE D 13 TRP 0.006 0.001 TRP E 415 HIS 0.002 0.000 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (15105) covalent geometry : angle 0.59547 / 0.29 (20320) SS BOND : bond 0.00130 / 0.07 ( 5) SS BOND : angle 2.36284 / 1.27 ( 10) hydrogen bonds : bond 0.04074 / 2.81 ( 665) hydrogen bonds : angle 3.85251 / 2.63 ( 2340) link_BETA1-4 : bond 0.00327 / 0.16 ( 5) link_BETA1-4 : angle 1.20115 / 0.71 ( 15) link_NAG-ASN : bond 0.00187 / 0.10 ( 5) link_NAG-ASN : angle 0.34845 / 0.20 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4601.08 seconds wall clock time: 94 minutes 41.48 seconds (5681.48 seconds total)