Starting phenix.real_space_refine on Sun Jul 5 07:34:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwc_44964/07_2026/9bwc_44964.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwc_44964/07_2026/9bwc_44964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bwc_44964/07_2026/9bwc_44964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwc_44964/07_2026/9bwc_44964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bwc_44964/07_2026/9bwc_44964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwc_44964/07_2026/9bwc_44964.map" } resolution = 2.19 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= 0.003 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 14705 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 9625 2.51 5 N 2340 2.21 5 O 2675 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: 14740 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2833 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 bond proxies already assigned to first conformer: 2883 Chain: "B" Number of atoms: 2833 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 bond proxies already assigned to first conformer: 2883 Chain: "C" Number of atoms: 2833 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 bond proxies already assigned to first conformer: 2883 Chain: "D" Number of atoms: 2833 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 bond proxies already assigned to first conformer: 2883 Chain: "E" Number of atoms: 2833 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 bond proxies already assigned to first conformer: 2883 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: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 80 Unusual residues: {'PIO': 1, 'PX4': 5} Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PX4:plan-2': 4, 'PIO:plan-1': 1, 'PX4:plan-1': 1} Unresolved non-hydrogen planarities: 24 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'PIO': 1, 'PX4': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PX4:plan-2': 4, 'PIO:plan-1': 1, 'PX4:plan-1': 1} Unresolved non-hydrogen planarities: 24 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'PIO': 1, 'PX4': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PX4:plan-2': 4, 'PIO:plan-1': 1, 'PX4:plan-1': 1} Unresolved non-hydrogen planarities: 24 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'PIO': 1, 'PX4': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PX4:plan-2': 4, 'PIO:plan-1': 1, 'PX4:plan-1': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 80 Unusual residues: {'PIO': 1, 'PX4': 5} Inner-chain residues flagged as termini: ['pdbres="GLY E 505 "'] Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PX4:plan-2': 4, 'PX4:plan-1': 1, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AARG A 65 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 65 " occ=0.50 residue: pdb=" N AARG B 65 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 65 " occ=0.50 residue: pdb=" N AARG C 65 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 65 " occ=0.50 residue: pdb=" N AARG D 65 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 65 " occ=0.50 residue: pdb=" N AARG E 65 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 65 " occ=0.50 Time building chain proxies: 5.25, per 1000 atoms: 0.36 Number of scatterers: 14740 At special positions: 0 Unit cell: (99.12, 99.12, 132.72, 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 2675 8.00 N 2340 7.00 C 9625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3350 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 40.1% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 71 through 74 removed outlier: 3.561A pdb=" N ALA A 74 " --> pdb=" O PRO A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.838A pdb=" N LEU A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.506A pdb=" N TRP A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.626A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 420 removed outlier: 3.969A 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 18 Processing helix chain 'B' and resid 71 through 74 removed outlier: 3.561A pdb=" N ALA B 74 " --> pdb=" O PRO B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.839A pdb=" N LEU B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 93 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 240 removed outlier: 3.506A pdb=" N TRP B 239 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.626A pdb=" N LEU B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 420 removed outlier: 3.969A 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 18 Processing helix chain 'C' and resid 71 through 74 removed outlier: 3.561A pdb=" N ALA C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 86 through 93 removed outlier: 3.839A pdb=" N LEU C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 227 through 240 removed outlier: 3.507A pdb=" N TRP C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 244 Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.626A pdb=" N LEU C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 420 removed outlier: 3.969A 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 18 Processing helix chain 'D' and resid 71 through 74 removed outlier: 3.560A pdb=" N ALA D 74 " --> pdb=" O PRO D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.838A pdb=" N LEU D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 227 through 240 removed outlier: 3.506A pdb=" N TRP D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 240 " --> pdb=" O ILE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 244 Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.626A pdb=" N LEU D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 420 removed outlier: 3.969A 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 18 Processing helix chain 'E' and resid 71 through 74 removed outlier: 3.561A pdb=" N ALA E 74 " --> pdb=" O PRO E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 74' Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.838A pdb=" N LEU E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE E 93 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 147 Processing helix chain 'E' and resid 220 through 227 Processing helix chain 'E' and resid 227 through 240 removed outlier: 3.506A pdb=" N TRP E 239 " --> pdb=" O VAL E 235 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL E 240 " --> pdb=" O ILE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.626A pdb=" N LEU E 298 " --> pdb=" O VAL E 294 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 420 removed outlier: 3.969A 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 85 removed outlier: 4.606A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.554A 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 108 removed outlier: 6.516A pdb=" N THR A 135 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA A 106 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 133 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N PHE A 108 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ARG A 131 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.554A 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 200 through 201 Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 85 removed outlier: 4.606A pdb=" N LEU B 118 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 108 removed outlier: 6.516A pdb=" N THR B 135 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA B 106 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR B 133 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N PHE B 108 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ARG B 131 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AA8, first strand: chain 'B' and resid 200 through 201 Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 85 removed outlier: 4.606A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 108 removed outlier: 6.517A pdb=" N THR C 135 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA C 106 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR C 133 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N PHE C 108 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ARG C 131 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 Processing sheet with id=AB3, first strand: chain 'C' and resid 200 through 201 Processing sheet with id=AB4, first strand: chain 'D' and resid 82 through 85 removed outlier: 4.606A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 103 through 108 removed outlier: 6.516A pdb=" N THR D 135 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA D 106 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR D 133 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N PHE D 108 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ARG D 131 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 98 through 100 Processing sheet with id=AB7, first strand: chain 'D' and resid 200 through 201 Processing sheet with id=AB8, first strand: chain 'E' and resid 82 through 85 removed outlier: 4.606A pdb=" N LEU E 118 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 103 through 108 removed outlier: 6.516A pdb=" N THR E 135 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA E 106 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR E 133 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N PHE E 108 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ARG E 131 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 100 Processing sheet with id=AC2, first strand: chain 'E' and resid 200 through 201 820 hydrogen bonds defined for protein. 2380 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: 2.68 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2280 1.31 - 1.44: 4185 1.44 - 1.56: 8410 1.56 - 1.69: 0 1.69 - 1.82: 165 Bond restraints: 15040 Sorted by residual: bond pdb=" C PRO B 146 " pdb=" O PRO B 146 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.26e-02 6.30e+03 1.66e+01 bond pdb=" C PRO E 146 " pdb=" O PRO E 146 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.26e-02 6.30e+03 1.66e+01 bond pdb=" C PRO D 146 " pdb=" O PRO D 146 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.26e-02 6.30e+03 1.66e+01 bond pdb=" C PRO A 146 " pdb=" O PRO A 146 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.26e-02 6.30e+03 1.65e+01 bond pdb=" C PRO C 146 " pdb=" O PRO C 146 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.26e-02 6.30e+03 1.64e+01 ... (remaining 15035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 19415 1.92 - 3.85: 691 3.85 - 5.77: 104 5.77 - 7.70: 45 7.70 - 9.62: 25 Bond angle restraints: 20280 Sorted by residual: angle pdb=" N PRO C 146 " pdb=" CA PRO C 146 " pdb=" C PRO C 146 " ideal model delta sigma weight residual 113.53 103.91 9.62 1.39e+00 5.18e-01 4.79e+01 angle pdb=" N PRO A 146 " pdb=" CA PRO A 146 " pdb=" C PRO A 146 " ideal model delta sigma weight residual 113.53 103.91 9.62 1.39e+00 5.18e-01 4.79e+01 angle pdb=" N PRO D 146 " pdb=" CA PRO D 146 " pdb=" C PRO D 146 " ideal model delta sigma weight residual 113.53 103.92 9.61 1.39e+00 5.18e-01 4.78e+01 angle pdb=" N PRO E 146 " pdb=" CA PRO E 146 " pdb=" C PRO E 146 " ideal model delta sigma weight residual 113.53 103.92 9.61 1.39e+00 5.18e-01 4.78e+01 angle pdb=" N PRO B 146 " pdb=" CA PRO B 146 " pdb=" C PRO B 146 " ideal model delta sigma weight residual 113.53 103.93 9.60 1.39e+00 5.18e-01 4.77e+01 ... (remaining 20275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 8095 15.74 - 31.49: 806 31.49 - 47.23: 199 47.23 - 62.97: 15 62.97 - 78.72: 20 Dihedral angle restraints: 9135 sinusoidal: 3980 harmonic: 5155 Sorted by residual: dihedral pdb=" CA ILE D 62 " pdb=" C ILE D 62 " pdb=" N PHE D 63 " pdb=" CA PHE D 63 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ILE C 62 " pdb=" C ILE C 62 " pdb=" N PHE C 63 " pdb=" CA PHE C 63 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ILE B 62 " pdb=" C ILE B 62 " pdb=" N PHE B 63 " pdb=" CA PHE B 63 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 9132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2046 0.091 - 0.182: 169 0.182 - 0.273: 25 0.273 - 0.364: 5 0.364 - 0.455: 5 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CA PHE C 145 " pdb=" N PHE C 145 " pdb=" C PHE C 145 " pdb=" CB PHE C 145 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CA PHE E 145 " pdb=" N PHE E 145 " pdb=" C PHE E 145 " pdb=" CB PHE E 145 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.14e+00 chirality pdb=" CA PHE A 145 " pdb=" N PHE A 145 " pdb=" C PHE A 145 " pdb=" CB PHE A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.12e+00 ... (remaining 2247 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 144 " -0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C ASN E 144 " 0.068 2.00e-02 2.50e+03 pdb=" O ASN E 144 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE E 145 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 144 " -0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C ASN B 144 " 0.068 2.00e-02 2.50e+03 pdb=" O ASN B 144 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE B 145 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 144 " -0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C ASN A 144 " 0.068 2.00e-02 2.50e+03 pdb=" O ASN A 144 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE A 145 " -0.023 2.00e-02 2.50e+03 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 100 2.52 - 3.12: 9962 3.12 - 3.71: 22069 3.71 - 4.31: 33483 4.31 - 4.90: 55269 Nonbonded interactions: 120883 Sorted by model distance: nonbonded pdb=" CG1 VAL C 111 " pdb=" O HOH B 601 " model vdw 1.925 3.460 nonbonded pdb=" CG1 VAL A 111 " pdb=" O HOH E 601 " model vdw 1.925 3.460 nonbonded pdb=" CG1 VAL E 111 " pdb=" O HOH D 601 " model vdw 1.925 3.460 nonbonded pdb=" CG1 VAL B 111 " pdb=" O HOH A 701 " model vdw 1.925 3.460 nonbonded pdb=" CG1 VAL D 111 " pdb=" O HOH C 601 " model vdw 1.926 3.460 ... (remaining 120878 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 64 or resid 66 through 427 or (resid 604 and (na \ me C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C17 or name C18 or name C9 or name O5 or name O6 )))) selection = (chain 'B' and (resid 8 through 64 or resid 66 through 427 or resid 504)) selection = (chain 'C' and (resid 8 through 64 or resid 66 through 427 or resid 504)) selection = (chain 'D' and (resid 8 through 64 or resid 66 through 427 or resid 504)) selection = (chain 'E' and (resid 8 through 64 or resid 66 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=0.50 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.940 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 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 : 0.005 0.051 15050 Z= 0.324 Angle : 0.910 9.623 20310 Z= 0.546 Chirality : 0.059 0.455 2250 Planarity : 0.008 0.048 2520 Dihedral : 13.545 78.717 5785 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.21 % Allowed : 11.17 % Favored : 87.62 % 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: -2.21 (0.18), residues: 1725 helix: -2.79 (0.14), residues: 580 sheet: 0.14 (0.24), residues: 475 loop : -1.21 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.002 ARG C 271 TYR 0.018 0.002 TYR E 301 PHE 0.019 0.001 PHE E 295 TRP 0.007 0.001 TRP C 415 HIS 0.002 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.32 (15040) covalent geometry : angle 0.90964 / 0.55 (20280) hydrogen bonds : bond 0.16625 / 10.98 ( 715) hydrogen bonds : angle 6.73878 / 4.67 ( 2380) link_BETA1-4 : bond 0.00339 / 0.18 ( 5) link_BETA1-4 : angle 1.19848 / 0.73 ( 15) link_NAG-ASN : bond 0.00125 / 0.07 ( 5) link_NAG-ASN : angle 1.17225 / 0.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.495 Fit side-chains REVERT: A 78 TYR cc_start: 0.7900 (t80) cc_final: 0.7683 (t80) REVERT: B 177 GLN cc_start: 0.8741 (mt0) cc_final: 0.8527 (mt0) REVERT: E 226 GLN cc_start: 0.8467 (tp40) cc_final: 0.8249 (tp40) REVERT: E 287 MET cc_start: 0.8553 (mmm) cc_final: 0.8353 (mmm) outliers start: 19 outliers final: 8 residues processed: 196 average time/residue: 0.5326 time to fit residues: 115.5212 Evaluate side-chains 183 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain E residue 240 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 245 ASN E 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.095884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.064494 restraints weight = 75103.384| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.98 r_work: 0.2581 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9226 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15050 Z= 0.161 Angle : 0.629 6.926 20310 Z= 0.332 Chirality : 0.045 0.150 2250 Planarity : 0.007 0.123 2520 Dihedral : 5.754 50.472 2376 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.48 % Allowed : 13.14 % Favored : 84.38 % 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: 0.02 (0.19), residues: 1725 helix: 0.65 (0.20), residues: 575 sheet: 0.49 (0.24), residues: 475 loop : -0.80 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.024 0.002 TYR D 301 PHE 0.020 0.002 PHE E 295 TRP 0.010 0.001 TRP C 415 HIS 0.004 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (15040) covalent geometry : angle 0.62785 / 0.33 (20280) hydrogen bonds : bond 0.05656 / 3.75 ( 715) hydrogen bonds : angle 4.51109 / 3.10 ( 2380) link_BETA1-4 : bond 0.00238 / 0.13 ( 5) link_BETA1-4 : angle 0.97236 / 0.61 ( 15) link_NAG-ASN : bond 0.00060 / 0.04 ( 5) link_NAG-ASN : angle 1.01240 / 0.58 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.554 Fit side-chains REVERT: A 18 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8109 (mtm) REVERT: A 78 TYR cc_start: 0.8182 (t80) cc_final: 0.7766 (t80) REVERT: B 132 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9165 (pp) REVERT: B 177 GLN cc_start: 0.9155 (mt0) cc_final: 0.8951 (mt0) REVERT: D 386 LYS cc_start: 0.5870 (OUTLIER) cc_final: 0.4480 (pmtt) REVERT: E 226 GLN cc_start: 0.8897 (tp40) cc_final: 0.8679 (tp40) REVERT: E 386 LYS cc_start: 0.5633 (OUTLIER) cc_final: 0.4489 (pmtt) outliers start: 39 outliers final: 17 residues processed: 201 average time/residue: 0.5752 time to fit residues: 127.2627 Evaluate side-chains 200 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain E residue 417 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 100 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.098511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.067529 restraints weight = 71185.475| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.90 r_work: 0.2649 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15050 Z= 0.106 Angle : 0.561 6.717 20310 Z= 0.291 Chirality : 0.043 0.154 2250 Planarity : 0.005 0.092 2520 Dihedral : 5.119 50.398 2372 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.22 % Allowed : 14.16 % Favored : 83.62 % 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: 0.87 (0.20), residues: 1725 helix: 1.77 (0.20), residues: 575 sheet: 0.78 (0.26), residues: 475 loop : -0.59 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.022 0.002 TYR D 301 PHE 0.018 0.001 PHE D 295 TRP 0.009 0.001 TRP B 68 HIS 0.002 0.000 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (15040) covalent geometry : angle 0.56046 / 0.29 (20280) hydrogen bonds : bond 0.04322 / 2.88 ( 715) hydrogen bonds : angle 4.00399 / 2.74 ( 2380) link_BETA1-4 : bond 0.00282 / 0.15 ( 5) link_BETA1-4 : angle 1.03566 / 0.63 ( 15) link_NAG-ASN : bond 0.00111 / 0.06 ( 5) link_NAG-ASN : angle 0.73105 / 0.42 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.545 Fit side-chains REVERT: A 78 TYR cc_start: 0.8174 (t80) cc_final: 0.7870 (t80) REVERT: B 132 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9183 (pp) REVERT: B 226 GLN cc_start: 0.8792 (tp40) cc_final: 0.8583 (tp40) REVERT: E 18 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7904 (mtm) REVERT: E 27 ARG cc_start: 0.9272 (mtm180) cc_final: 0.8990 (mtp180) REVERT: E 226 GLN cc_start: 0.8740 (tp40) cc_final: 0.8481 (tp40) outliers start: 35 outliers final: 11 residues processed: 202 average time/residue: 0.5622 time to fit residues: 124.8694 Evaluate side-chains 194 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 107 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.065776 restraints weight = 78690.187| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 4.03 r_work: 0.2607 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15050 Z= 0.131 Angle : 0.576 6.620 20310 Z= 0.301 Chirality : 0.043 0.157 2250 Planarity : 0.005 0.092 2520 Dihedral : 4.875 26.060 2365 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.48 % Allowed : 14.10 % Favored : 83.43 % 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 (0.20), residues: 1725 helix: 2.08 (0.20), residues: 575 sheet: 0.83 (0.25), residues: 495 loop : -0.43 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 20 TYR 0.026 0.002 TYR D 301 PHE 0.019 0.001 PHE E 295 TRP 0.008 0.001 TRP C 415 HIS 0.003 0.001 HIS D 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (15040) covalent geometry : angle 0.57555 / 0.30 (20280) hydrogen bonds : bond 0.04584 / 3.04 ( 715) hydrogen bonds : angle 3.99024 / 2.73 ( 2380) link_BETA1-4 : bond 0.00227 / 0.12 ( 5) link_BETA1-4 : angle 1.09621 / 0.68 ( 15) link_NAG-ASN : bond 0.00049 / 0.03 ( 5) link_NAG-ASN : angle 0.73530 / 0.41 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.497 Fit side-chains REVERT: A 8 MET cc_start: 0.6102 (ttm) cc_final: 0.5819 (ttt) REVERT: A 186 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8922 (mm110) REVERT: B 132 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9169 (pp) outliers start: 39 outliers final: 16 residues processed: 200 average time/residue: 0.5361 time to fit residues: 117.8667 Evaluate side-chains 194 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 417 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.3980 chunk 129 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.097834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.067213 restraints weight = 67031.749| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.78 r_work: 0.2645 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9183 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15050 Z= 0.108 Angle : 0.546 7.790 20310 Z= 0.282 Chirality : 0.042 0.155 2250 Planarity : 0.003 0.075 2520 Dihedral : 4.711 25.914 2365 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.78 % Allowed : 15.37 % Favored : 82.86 % 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: 1.35 (0.20), residues: 1725 helix: 2.28 (0.21), residues: 580 sheet: 1.00 (0.26), residues: 475 loop : -0.40 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 271 TYR 0.023 0.001 TYR D 301 PHE 0.018 0.001 PHE E 295 TRP 0.008 0.001 TRP D 68 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15040) covalent geometry : angle 0.54564 / 0.28 (20280) hydrogen bonds : bond 0.04118 / 2.74 ( 715) hydrogen bonds : angle 3.83732 / 2.63 ( 2380) link_BETA1-4 : bond 0.00269 / 0.15 ( 5) link_BETA1-4 : angle 1.08582 / 0.66 ( 15) link_NAG-ASN : bond 0.00132 / 0.07 ( 5) link_NAG-ASN : angle 0.65121 / 0.36 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.445 Fit side-chains REVERT: A 8 MET cc_start: 0.6134 (ttm) cc_final: 0.5691 (ttt) REVERT: A 186 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8909 (mm110) REVERT: B 132 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9171 (pp) REVERT: B 177 GLN cc_start: 0.9057 (mt0) cc_final: 0.8852 (mt0) outliers start: 28 outliers final: 13 residues processed: 196 average time/residue: 0.5482 time to fit residues: 118.7462 Evaluate side-chains 194 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 37 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.097600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.066933 restraints weight = 71334.779| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.88 r_work: 0.2634 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9190 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15050 Z= 0.109 Angle : 0.546 7.807 20310 Z= 0.282 Chirality : 0.043 0.156 2250 Planarity : 0.003 0.026 2520 Dihedral : 4.700 27.542 2365 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.46 % Allowed : 15.87 % Favored : 82.67 % 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: 1.46 (0.20), residues: 1725 helix: 2.39 (0.21), residues: 580 sheet: 1.03 (0.26), residues: 475 loop : -0.32 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 20 TYR 0.024 0.001 TYR D 301 PHE 0.018 0.001 PHE A 295 TRP 0.008 0.001 TRP E 68 HIS 0.002 0.001 HIS D 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (15040) covalent geometry : angle 0.54565 / 0.28 (20280) hydrogen bonds : bond 0.04144 / 2.75 ( 715) hydrogen bonds : angle 3.81572 / 2.61 ( 2380) link_BETA1-4 : bond 0.00287 / 0.16 ( 5) link_BETA1-4 : angle 1.10835 / 0.68 ( 15) link_NAG-ASN : bond 0.00119 / 0.07 ( 5) link_NAG-ASN : angle 0.65285 / 0.36 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.507 Fit side-chains REVERT: A 8 MET cc_start: 0.6254 (ttm) cc_final: 0.5931 (ttt) REVERT: B 132 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9166 (pp) REVERT: B 177 GLN cc_start: 0.9064 (mt0) cc_final: 0.8850 (mt0) outliers start: 23 outliers final: 14 residues processed: 191 average time/residue: 0.5649 time to fit residues: 118.8282 Evaluate side-chains 193 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 109 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN D 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.065665 restraints weight = 64413.643| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.72 r_work: 0.2612 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9205 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15050 Z= 0.132 Angle : 0.564 7.872 20310 Z= 0.293 Chirality : 0.043 0.157 2250 Planarity : 0.003 0.026 2520 Dihedral : 4.853 30.351 2365 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.52 % Allowed : 15.75 % Favored : 82.73 % 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: 1.54 (0.20), residues: 1725 helix: 2.48 (0.20), residues: 580 sheet: 1.06 (0.26), residues: 475 loop : -0.29 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 20 TYR 0.026 0.002 TYR D 301 PHE 0.019 0.001 PHE E 295 TRP 0.007 0.001 TRP E 68 HIS 0.003 0.001 HIS D 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (15040) covalent geometry : angle 0.56338 / 0.29 (20280) hydrogen bonds : bond 0.04475 / 2.97 ( 715) hydrogen bonds : angle 3.87725 / 2.65 ( 2380) link_BETA1-4 : bond 0.00278 / 0.15 ( 5) link_BETA1-4 : angle 1.10407 / 0.68 ( 15) link_NAG-ASN : bond 0.00077 / 0.05 ( 5) link_NAG-ASN : angle 0.74223 / 0.41 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.585 Fit side-chains REVERT: A 8 MET cc_start: 0.6188 (ttm) cc_final: 0.5862 (ttt) REVERT: B 132 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9162 (pp) REVERT: B 177 GLN cc_start: 0.9066 (mt0) cc_final: 0.8865 (mt0) REVERT: E 18 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.8047 (mtm) outliers start: 24 outliers final: 18 residues processed: 180 average time/residue: 0.5446 time to fit residues: 108.4545 Evaluate side-chains 191 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 62 optimal weight: 3.9990 chunk 121 optimal weight: 0.0980 chunk 136 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN A 226 GLN C 226 GLN D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.066960 restraints weight = 51974.928| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.42 r_work: 0.2646 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9187 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15050 Z= 0.115 Angle : 0.554 7.895 20310 Z= 0.286 Chirality : 0.043 0.159 2250 Planarity : 0.003 0.026 2520 Dihedral : 4.850 33.861 2365 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.33 % Allowed : 15.94 % Favored : 82.73 % 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: 1.68 (0.21), residues: 1725 helix: 2.63 (0.20), residues: 580 sheet: 1.07 (0.26), residues: 475 loop : -0.20 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 20 TYR 0.025 0.001 TYR D 301 PHE 0.018 0.001 PHE E 295 TRP 0.008 0.001 TRP D 68 HIS 0.002 0.001 HIS D 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (15040) covalent geometry : angle 0.55335 / 0.29 (20280) hydrogen bonds : bond 0.04228 / 2.81 ( 715) hydrogen bonds : angle 3.81464 / 2.61 ( 2380) link_BETA1-4 : bond 0.00279 / 0.15 ( 5) link_BETA1-4 : angle 1.06503 / 0.65 ( 15) link_NAG-ASN : bond 0.00121 / 0.07 ( 5) link_NAG-ASN : angle 0.69941 / 0.39 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.602 Fit side-chains REVERT: A 8 MET cc_start: 0.6149 (ttm) cc_final: 0.5829 (ttt) REVERT: B 132 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9157 (pp) REVERT: B 177 GLN cc_start: 0.9040 (mt0) cc_final: 0.8836 (mt0) outliers start: 21 outliers final: 16 residues processed: 181 average time/residue: 0.5130 time to fit residues: 103.0181 Evaluate side-chains 189 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 220 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 162 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 120 optimal weight: 0.0070 chunk 108 optimal weight: 0.0270 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 146 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN C 226 GLN D 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.068991 restraints weight = 69093.138| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.81 r_work: 0.2684 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15050 Z= 0.093 Angle : 0.535 7.946 20310 Z= 0.273 Chirality : 0.042 0.151 2250 Planarity : 0.003 0.027 2520 Dihedral : 4.572 34.636 2365 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.95 % Allowed : 16.19 % Favored : 82.86 % 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: 1.83 (0.21), residues: 1725 helix: 2.73 (0.21), residues: 585 sheet: 1.35 (0.26), residues: 450 loop : -0.22 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 20 TYR 0.020 0.001 TYR D 301 PHE 0.017 0.001 PHE E 295 TRP 0.009 0.001 TRP D 68 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (15040) covalent geometry : angle 0.53450 / 0.27 (20280) hydrogen bonds : bond 0.03532 / 2.36 ( 715) hydrogen bonds : angle 3.62319 / 2.47 ( 2380) link_BETA1-4 : bond 0.00305 / 0.17 ( 5) link_BETA1-4 : angle 1.09455 / 0.67 ( 15) link_NAG-ASN : bond 0.00190 / 0.10 ( 5) link_NAG-ASN : angle 0.47868 / 0.27 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.563 Fit side-chains REVERT: B 386 LYS cc_start: 0.5375 (pmtt) cc_final: 0.5084 (mtmt) REVERT: E 245 ASN cc_start: 0.8302 (t0) cc_final: 0.8084 (t0) outliers start: 15 outliers final: 9 residues processed: 186 average time/residue: 0.4776 time to fit residues: 99.0242 Evaluate side-chains 182 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 145 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 1 optimal weight: 0.0980 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN C 226 GLN D 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.098297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.068188 restraints weight = 59020.925| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.61 r_work: 0.2670 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15050 Z= 0.103 Angle : 0.548 8.162 20310 Z= 0.280 Chirality : 0.042 0.153 2250 Planarity : 0.003 0.041 2520 Dihedral : 4.611 35.171 2365 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.57 % Allowed : 16.32 % Favored : 83.11 % 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: 1.89 (0.21), residues: 1725 helix: 2.84 (0.21), residues: 580 sheet: 1.13 (0.26), residues: 475 loop : -0.06 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 20 TYR 0.024 0.001 TYR D 301 PHE 0.018 0.001 PHE D 121 TRP 0.007 0.001 TRP E 68 HIS 0.003 0.001 HIS E 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (15040) covalent geometry : angle 0.54717 / 0.28 (20280) hydrogen bonds : bond 0.03812 / 2.54 ( 715) hydrogen bonds : angle 3.64673 / 2.49 ( 2380) link_BETA1-4 : bond 0.00263 / 0.15 ( 5) link_BETA1-4 : angle 1.08662 / 0.66 ( 15) link_NAG-ASN : bond 0.00139 / 0.08 ( 5) link_NAG-ASN : angle 0.54371 / 0.30 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.537 Fit side-chains REVERT: B 386 LYS cc_start: 0.5441 (pmtt) cc_final: 0.5159 (mtmt) REVERT: E 245 ASN cc_start: 0.8306 (t0) cc_final: 0.8080 (t0) outliers start: 9 outliers final: 8 residues processed: 178 average time/residue: 0.5078 time to fit residues: 100.2668 Evaluate side-chains 182 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 10 optimal weight: 2.9990 chunk 159 optimal weight: 0.2980 chunk 102 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN B 226 GLN C 226 GLN D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.096095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.065331 restraints weight = 66453.425| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.79 r_work: 0.2600 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9213 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15050 Z= 0.142 Angle : 0.583 8.160 20310 Z= 0.303 Chirality : 0.044 0.161 2250 Planarity : 0.003 0.038 2520 Dihedral : 4.991 38.553 2365 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.70 % Allowed : 16.32 % Favored : 82.98 % 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: 1.84 (0.21), residues: 1725 helix: 2.73 (0.21), residues: 585 sheet: 1.11 (0.26), residues: 475 loop : -0.05 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 20 TYR 0.028 0.002 TYR C 301 PHE 0.019 0.002 PHE E 295 TRP 0.011 0.001 TRP E 170 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (15040) covalent geometry : angle 0.58188 / 0.30 (20280) hydrogen bonds : bond 0.04635 / 3.08 ( 715) hydrogen bonds : angle 3.87820 / 2.65 ( 2380) link_BETA1-4 : bond 0.00229 / 0.13 ( 5) link_BETA1-4 : angle 1.05093 / 0.65 ( 15) link_NAG-ASN : bond 0.00070 / 0.04 ( 5) link_NAG-ASN : angle 0.77514 / 0.43 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5510.84 seconds wall clock time: 94 minutes 36.89 seconds (5676.89 seconds total)