Starting phenix.real_space_refine on Sat Jun 21 15:56:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eis_28163/06_2025/8eis_28163_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eis_28163/06_2025/8eis_28163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eis_28163/06_2025/8eis_28163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eis_28163/06_2025/8eis_28163.map" model { file = "/net/cci-nas-00/data/ceres_data/8eis_28163/06_2025/8eis_28163_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eis_28163/06_2025/8eis_28163_trim.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 80 5.16 5 C 8115 2.51 5 N 1860 2.21 5 O 2290 1.98 5 H 12025 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24370 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4781 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "B" Number of atoms: 4781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4781 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "C" Number of atoms: 4781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4781 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "D" Number of atoms: 4781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4781 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "E" Number of atoms: 4781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4781 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {'DU0': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {'DU0': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {'DU0': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {'DU0': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {'DU0': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 11.98, per 1000 atoms: 0.49 Number of scatterers: 24370 At special positions: 0 Unit cell: (96.096, 97.152, 118.272, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 O 2290 8.00 N 1860 7.00 C 8115 6.00 H 12025 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 150 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 145 " distance=2.03 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 145 " distance=2.03 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 NAG-ASN " NAG A 401 " - " ASN A 77 " " NAG A 402 " - " ASN A 27 " " NAG A 403 " - " ASN A 180 " " NAG A 404 " - " ASN A 186 " " NAG B 401 " - " ASN B 77 " " NAG B 402 " - " ASN B 27 " " NAG B 403 " - " ASN B 180 " " NAG B 404 " - " ASN B 186 " " NAG C 401 " - " ASN C 77 " " NAG C 402 " - " ASN C 27 " " NAG C 403 " - " ASN C 180 " " NAG C 404 " - " ASN C 186 " " NAG D 401 " - " ASN D 77 " " NAG D 402 " - " ASN D 27 " " NAG D 403 " - " ASN D 180 " " NAG D 404 " - " ASN D 186 " " NAG E 401 " - " ASN E 77 " " NAG E 402 " - " ASN E 27 " " NAG E 403 " - " ASN E 180 " " NAG E 404 " - " ASN E 186 " Time building additional restraints: 6.34 Conformation dependent library (CDL) restraints added in 1.9 seconds 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2810 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 20 sheets defined 33.2% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.555A pdb=" N LEU A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 4.132A pdb=" N ASN A 76 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.821A pdb=" N ILE A 88 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 229 Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.523A pdb=" N ASP A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 292 Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.547A pdb=" N LEU B 15 " --> pdb=" O ARG B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 4.130A pdb=" N ASN B 76 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.839A pdb=" N ILE B 88 " --> pdb=" O LYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 229 Proline residue: B 215 - end of helix Processing helix chain 'B' and resid 235 through 256 removed outlier: 3.528A pdb=" N ASP B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 292 Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.560A pdb=" N LEU C 15 " --> pdb=" O ARG C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 4.106A pdb=" N ASN C 76 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.837A pdb=" N ILE C 88 " --> pdb=" O LYS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 229 removed outlier: 3.584A pdb=" N ILE C 210 " --> pdb=" O THR C 206 " (cutoff:3.500A) Proline residue: C 215 - end of helix Processing helix chain 'C' and resid 235 through 256 removed outlier: 3.528A pdb=" N ASP C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 292 Processing helix chain 'D' and resid 3 through 15 removed outlier: 3.628A pdb=" N LEU D 15 " --> pdb=" O ARG D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 removed outlier: 4.099A pdb=" N ASN D 76 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.840A pdb=" N ILE D 88 " --> pdb=" O LYS D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 229 removed outlier: 3.583A pdb=" N ILE D 210 " --> pdb=" O THR D 206 " (cutoff:3.500A) Proline residue: D 215 - end of helix Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.530A pdb=" N ASP D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 292 Processing helix chain 'E' and resid 3 through 15 removed outlier: 3.525A pdb=" N LEU E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 76 removed outlier: 4.161A pdb=" N ASN E 76 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.822A pdb=" N ILE E 88 " --> pdb=" O LYS E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 229 removed outlier: 3.585A pdb=" N ILE E 210 " --> pdb=" O THR E 206 " (cutoff:3.500A) Proline residue: E 215 - end of helix Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.516A pdb=" N ASP E 255 " --> pdb=" O LEU E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 292 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 83 removed outlier: 3.905A pdb=" N TRP A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 83 removed outlier: 3.905A pdb=" N TRP A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE A 52 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP A 45 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N MET A 54 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 43 " --> pdb=" O MET A 54 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG A 56 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE A 64 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP A 33 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ALA A 36 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 164 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 38 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR A 166 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU A 40 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP A 168 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N THR A 42 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 5.223A pdb=" N SER A 193 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 removed outlier: 5.223A pdb=" N SER A 193 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.926A pdb=" N TRP B 118 " --> pdb=" O THR B 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.926A pdb=" N TRP B 118 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE B 52 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP B 45 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N MET B 54 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU B 43 " --> pdb=" O MET B 54 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG B 56 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE B 64 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP B 33 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALA B 36 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU B 164 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 38 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR B 166 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU B 40 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP B 168 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N THR B 42 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 removed outlier: 5.190A pdb=" N SER B 193 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 94 removed outlier: 5.190A pdb=" N SER B 193 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.957A pdb=" N TRP C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.957A pdb=" N TRP C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE C 52 " --> pdb=" O ASP C 45 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASP C 45 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 54 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU C 43 " --> pdb=" O MET C 54 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG C 56 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE C 64 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP C 33 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ALA C 36 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 164 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU C 38 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR C 166 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU C 40 " --> pdb=" O TYR C 166 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP C 168 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N THR C 42 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 94 removed outlier: 5.146A pdb=" N SER C 193 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 93 through 94 removed outlier: 5.146A pdb=" N SER C 193 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 80 through 83 removed outlier: 3.892A pdb=" N TRP D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 80 through 83 removed outlier: 3.892A pdb=" N TRP D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE D 52 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP D 45 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N MET D 54 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU D 43 " --> pdb=" O MET D 54 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG D 56 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE D 64 " --> pdb=" O ASP D 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP D 33 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA D 36 " --> pdb=" O LYS D 162 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU D 164 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU D 38 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR D 166 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU D 40 " --> pdb=" O TYR D 166 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ASP D 168 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N THR D 42 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 93 through 94 removed outlier: 5.168A pdb=" N SER D 193 " --> pdb=" O VAL D 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 93 through 94 removed outlier: 5.168A pdb=" N SER D 193 " --> pdb=" O VAL D 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 80 through 83 removed outlier: 3.919A pdb=" N TRP E 118 " --> pdb=" O THR E 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 80 through 83 removed outlier: 3.919A pdb=" N TRP E 118 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 52 " --> pdb=" O ASP E 45 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASP E 45 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N MET E 54 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU E 43 " --> pdb=" O MET E 54 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG E 56 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE E 64 " --> pdb=" O ASP E 33 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP E 33 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ALA E 36 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU E 164 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU E 38 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR E 166 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU E 40 " --> pdb=" O TYR E 166 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASP E 168 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N THR E 42 " --> pdb=" O ASP E 168 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 94 removed outlier: 5.172A pdb=" N SER E 193 " --> pdb=" O VAL E 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 93 through 94 removed outlier: 5.172A pdb=" N SER E 193 " --> pdb=" O VAL E 151 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1947 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: 9.52 Time building geometry restraints manager: 7.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12025 1.03 - 1.23: 72 1.23 - 1.42: 4957 1.42 - 1.61: 7491 1.61 - 1.81: 140 Bond restraints: 24685 Sorted by residual: bond pdb=" C ALA A 211 " pdb=" O ALA A 211 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.17e-02 7.31e+03 1.82e+01 bond pdb=" C LEU A 213 " pdb=" N ILE A 214 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.13e-02 7.83e+03 1.33e+01 bond pdb=" CA ILE B 214 " pdb=" C ILE B 214 " ideal model delta sigma weight residual 1.524 1.561 -0.037 1.05e-02 9.07e+03 1.23e+01 bond pdb=" CA ALA A 211 " pdb=" C ALA A 211 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.30e-02 5.92e+03 1.10e+01 bond pdb=" CA ILE B 214 " pdb=" CB ILE B 214 " ideal model delta sigma weight residual 1.537 1.574 -0.036 1.29e-02 6.01e+03 8.00e+00 ... (remaining 24680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 43093 1.46 - 2.93: 1361 2.93 - 4.39: 114 4.39 - 5.86: 19 5.86 - 7.32: 3 Bond angle restraints: 44590 Sorted by residual: angle pdb=" N GLY A 208 " pdb=" CA GLY A 208 " pdb=" C GLY A 208 " ideal model delta sigma weight residual 112.73 105.74 6.99 1.20e+00 6.94e-01 3.39e+01 angle pdb=" N GLY B 208 " pdb=" CA GLY B 208 " pdb=" C GLY B 208 " ideal model delta sigma weight residual 113.37 106.05 7.32 1.34e+00 5.57e-01 2.98e+01 angle pdb=" N ILE B 214 " pdb=" CA ILE B 214 " pdb=" C ILE B 214 " ideal model delta sigma weight residual 108.88 116.12 -7.24 2.16e+00 2.14e-01 1.12e+01 angle pdb=" N ILE B 209 " pdb=" CA ILE B 209 " pdb=" C ILE B 209 " ideal model delta sigma weight residual 110.72 108.15 2.57 1.01e+00 9.80e-01 6.49e+00 angle pdb=" C ILE B 209 " pdb=" CA ILE B 209 " pdb=" CB ILE B 209 " ideal model delta sigma weight residual 112.22 108.88 3.34 1.38e+00 5.25e-01 5.86e+00 ... (remaining 44585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 11514 21.68 - 43.36: 631 43.36 - 65.04: 154 65.04 - 86.71: 6 86.71 - 108.39: 20 Dihedral angle restraints: 12325 sinusoidal: 7070 harmonic: 5255 Sorted by residual: dihedral pdb=" CB CYS D 96 " pdb=" SG CYS D 96 " pdb=" SG CYS D 150 " pdb=" CB CYS D 150 " ideal model delta sinusoidal sigma weight residual 93.00 179.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sinusoidal sigma weight residual 93.00 177.89 -84.89 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS B 96 " pdb=" SG CYS B 96 " pdb=" SG CYS B 150 " pdb=" CB CYS B 150 " ideal model delta sinusoidal sigma weight residual 93.00 177.74 -84.74 1 1.00e+01 1.00e-02 8.72e+01 ... (remaining 12322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1918 0.082 - 0.165: 198 0.165 - 0.247: 2 0.247 - 0.329: 2 0.329 - 0.412: 5 Chirality restraints: 2125 Sorted by residual: chirality pdb=" C12 DU0 C 405 " pdb=" C11 DU0 C 405 " pdb=" C13 DU0 C 405 " pdb=" C14 DU0 C 405 " both_signs ideal model delta sigma weight residual False 2.59 2.18 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" C12 DU0 E 405 " pdb=" C11 DU0 E 405 " pdb=" C13 DU0 E 405 " pdb=" C14 DU0 E 405 " both_signs ideal model delta sigma weight residual False 2.59 2.18 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C12 DU0 A 405 " pdb=" C11 DU0 A 405 " pdb=" C13 DU0 A 405 " pdb=" C14 DU0 A 405 " both_signs ideal model delta sigma weight residual False 2.59 2.18 0.41 2.00e-01 2.50e+01 4.17e+00 ... (remaining 2122 not shown) Planarity restraints: 3425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 213 " 0.024 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C LEU A 213 " -0.082 2.00e-02 2.50e+03 pdb=" O LEU A 213 " 0.031 2.00e-02 2.50e+03 pdb=" N ILE A 214 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 206 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C THR A 206 " 0.046 2.00e-02 2.50e+03 pdb=" O THR A 206 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 207 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 264 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO C 265 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " 0.032 5.00e-02 4.00e+02 ... (remaining 3422 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 598 2.13 - 2.75: 45080 2.75 - 3.37: 67767 3.37 - 3.98: 91437 3.98 - 4.60: 141303 Nonbonded interactions: 346185 Sorted by model distance: nonbonded pdb="HH22 ARG A 11 " pdb=" O TYR A 82 " model vdw 1.517 2.450 nonbonded pdb="HH22 ARG B 11 " pdb=" O TYR B 82 " model vdw 1.536 2.450 nonbonded pdb="HH22 ARG C 11 " pdb=" O TYR C 82 " model vdw 1.545 2.450 nonbonded pdb="HH22 ARG D 11 " pdb=" O TYR D 82 " model vdw 1.555 2.450 nonbonded pdb="HH22 ARG E 11 " pdb=" O TYR E 82 " model vdw 1.587 2.450 ... (remaining 346180 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.440 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 52.970 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 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:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.007 0.055 12690 Z= 0.296 Angle : 0.709 7.320 17380 Z= 0.376 Chirality : 0.052 0.412 2125 Planarity : 0.006 0.058 2020 Dihedral : 14.603 108.394 5325 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1450 helix: 3.15 (0.24), residues: 395 sheet: -0.01 (0.23), residues: 425 loop : -0.81 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 63 HIS 0.012 0.003 HIS C 128 PHE 0.014 0.002 PHE E 244 TYR 0.021 0.002 TYR B 58 ARG 0.006 0.001 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 20) link_NAG-ASN : angle 1.77185 ( 60) hydrogen bonds : bond 0.10943 ( 594) hydrogen bonds : angle 5.10686 ( 1947) SS BOND : bond 0.00228 ( 10) SS BOND : angle 1.86648 ( 20) covalent geometry : bond 0.00663 (12660) covalent geometry : angle 0.69959 (17300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 173 GLN cc_start: 0.7992 (mt0) cc_final: 0.7791 (mm110) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 2.2837 time to fit residues: 388.3161 Evaluate side-chains 123 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN C 134 ASN D 134 ASN E 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.158840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106062 restraints weight = 39659.139| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.23 r_work: 0.3152 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12690 Z= 0.147 Angle : 0.621 7.234 17380 Z= 0.317 Chirality : 0.043 0.154 2125 Planarity : 0.004 0.039 2020 Dihedral : 9.454 63.166 2480 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.81 % Allowed : 6.32 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1450 helix: 3.16 (0.23), residues: 405 sheet: 0.01 (0.24), residues: 415 loop : -0.73 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.008 0.002 HIS D 128 PHE 0.025 0.002 PHE D 244 TYR 0.014 0.001 TYR B 58 ARG 0.007 0.001 ARG E 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 20) link_NAG-ASN : angle 1.52361 ( 60) hydrogen bonds : bond 0.04412 ( 594) hydrogen bonds : angle 4.60034 ( 1947) SS BOND : bond 0.00063 ( 10) SS BOND : angle 0.70734 ( 20) covalent geometry : bond 0.00342 (12660) covalent geometry : angle 0.61511 (17300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 173 GLN cc_start: 0.8156 (mt0) cc_final: 0.7699 (mm110) outliers start: 11 outliers final: 10 residues processed: 139 average time/residue: 2.1470 time to fit residues: 332.2325 Evaluate side-chains 136 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 123 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 81 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN C 134 ASN E 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.159662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106901 restraints weight = 39374.437| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.23 r_work: 0.3199 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12690 Z= 0.132 Angle : 0.594 7.639 17380 Z= 0.297 Chirality : 0.042 0.144 2125 Planarity : 0.004 0.047 2020 Dihedral : 7.488 49.940 2480 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.03 % Allowed : 9.19 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1450 helix: 3.41 (0.23), residues: 405 sheet: 0.05 (0.24), residues: 415 loop : -0.71 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 63 HIS 0.007 0.002 HIS D 128 PHE 0.020 0.001 PHE A 244 TYR 0.010 0.001 TYR E 75 ARG 0.004 0.000 ARG A 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00079 ( 20) link_NAG-ASN : angle 1.42424 ( 60) hydrogen bonds : bond 0.04010 ( 594) hydrogen bonds : angle 4.42791 ( 1947) SS BOND : bond 0.00091 ( 10) SS BOND : angle 0.59354 ( 20) covalent geometry : bond 0.00308 (12660) covalent geometry : angle 0.58951 (17300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 173 GLN cc_start: 0.8064 (mt0) cc_final: 0.7597 (mm110) outliers start: 14 outliers final: 6 residues processed: 142 average time/residue: 2.1451 time to fit residues: 340.9373 Evaluate side-chains 134 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 143 HIS B 134 ASN B 143 HIS C 134 ASN D 134 ASN E 143 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.159917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108550 restraints weight = 39488.457| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.18 r_work: 0.3163 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12690 Z= 0.234 Angle : 0.652 7.058 17380 Z= 0.327 Chirality : 0.044 0.140 2125 Planarity : 0.004 0.050 2020 Dihedral : 7.355 51.547 2480 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.74 % Allowed : 11.32 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1450 helix: 3.47 (0.23), residues: 405 sheet: 0.09 (0.23), residues: 425 loop : -0.80 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 118 HIS 0.006 0.002 HIS D 128 PHE 0.020 0.002 PHE A 244 TYR 0.013 0.001 TYR E 58 ARG 0.005 0.001 ARG A 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 20) link_NAG-ASN : angle 1.69261 ( 60) hydrogen bonds : bond 0.04052 ( 594) hydrogen bonds : angle 4.39734 ( 1947) SS BOND : bond 0.00135 ( 10) SS BOND : angle 1.03162 ( 20) covalent geometry : bond 0.00559 (12660) covalent geometry : angle 0.64508 (17300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 173 GLN cc_start: 0.8127 (mt0) cc_final: 0.7655 (mm110) outliers start: 10 outliers final: 9 residues processed: 138 average time/residue: 2.1634 time to fit residues: 333.2331 Evaluate side-chains 136 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 131 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 139 optimal weight: 0.0050 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 134 ASN C 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.158978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106198 restraints weight = 39819.189| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.26 r_work: 0.3198 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12690 Z= 0.127 Angle : 0.586 9.162 17380 Z= 0.293 Chirality : 0.042 0.146 2125 Planarity : 0.004 0.053 2020 Dihedral : 6.880 50.595 2480 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.96 % Allowed : 12.57 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.22), residues: 1450 helix: 3.60 (0.23), residues: 405 sheet: 0.14 (0.24), residues: 415 loop : -0.72 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 63 HIS 0.006 0.002 HIS D 128 PHE 0.021 0.001 PHE B 244 TYR 0.009 0.001 TYR D 75 ARG 0.005 0.000 ARG A 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 20) link_NAG-ASN : angle 1.43411 ( 60) hydrogen bonds : bond 0.03756 ( 594) hydrogen bonds : angle 4.30954 ( 1947) SS BOND : bond 0.00078 ( 10) SS BOND : angle 0.43625 ( 20) covalent geometry : bond 0.00297 (12660) covalent geometry : angle 0.58107 (17300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 173 GLN cc_start: 0.8064 (mt0) cc_final: 0.7551 (mm110) outliers start: 13 outliers final: 8 residues processed: 139 average time/residue: 2.2817 time to fit residues: 354.0326 Evaluate side-chains 133 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 0.0670 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN C 134 ASN D 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.159379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106625 restraints weight = 39447.159| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.24 r_work: 0.3205 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12690 Z= 0.137 Angle : 0.579 8.505 17380 Z= 0.288 Chirality : 0.041 0.139 2125 Planarity : 0.004 0.056 2020 Dihedral : 6.507 48.999 2480 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.10 % Allowed : 13.53 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1450 helix: 3.69 (0.23), residues: 405 sheet: 0.22 (0.24), residues: 415 loop : -0.69 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 63 HIS 0.006 0.002 HIS D 128 PHE 0.014 0.001 PHE E 244 TYR 0.010 0.001 TYR B 75 ARG 0.005 0.000 ARG A 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00091 ( 20) link_NAG-ASN : angle 1.43976 ( 60) hydrogen bonds : bond 0.03640 ( 594) hydrogen bonds : angle 4.21471 ( 1947) SS BOND : bond 0.00094 ( 10) SS BOND : angle 0.57268 ( 20) covalent geometry : bond 0.00322 (12660) covalent geometry : angle 0.57419 (17300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7557 (mm-40) REVERT: D 173 GLN cc_start: 0.8059 (mt0) cc_final: 0.7524 (mm110) outliers start: 15 outliers final: 6 residues processed: 139 average time/residue: 2.2297 time to fit residues: 344.5682 Evaluate side-chains 134 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 27 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN B 173 GLN C 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.158380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.107464 restraints weight = 39550.344| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.18 r_work: 0.3189 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.004 0.048 12690 Z= 0.184 Angle : 0.610 8.430 17380 Z= 0.304 Chirality : 0.042 0.139 2125 Planarity : 0.004 0.057 2020 Dihedral : 6.603 49.623 2480 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.81 % Allowed : 14.41 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.22), residues: 1450 helix: 3.71 (0.23), residues: 405 sheet: 0.26 (0.24), residues: 415 loop : -0.75 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 118 HIS 0.005 0.002 HIS D 128 PHE 0.016 0.001 PHE D 244 TYR 0.010 0.001 TYR E 58 ARG 0.007 0.001 ARG A 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 20) link_NAG-ASN : angle 1.49389 ( 60) hydrogen bonds : bond 0.03715 ( 594) hydrogen bonds : angle 4.22069 ( 1947) SS BOND : bond 0.00126 ( 10) SS BOND : angle 0.74472 ( 20) covalent geometry : bond 0.00439 (12660) covalent geometry : angle 0.60435 (17300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 173 GLN cc_start: 0.8090 (mt0) cc_final: 0.7594 (mm110) outliers start: 11 outliers final: 9 residues processed: 133 average time/residue: 2.0731 time to fit residues: 307.1025 Evaluate side-chains 136 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 127 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN C 134 ASN E 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.158796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107958 restraints weight = 39438.322| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.16 r_work: 0.3161 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12690 Z= 0.155 Angle : 0.587 8.585 17380 Z= 0.294 Chirality : 0.042 0.141 2125 Planarity : 0.004 0.050 2020 Dihedral : 6.495 49.569 2480 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.66 % Allowed : 14.71 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.22), residues: 1450 helix: 3.77 (0.23), residues: 405 sheet: 0.26 (0.24), residues: 415 loop : -0.73 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 118 HIS 0.005 0.002 HIS D 128 PHE 0.012 0.001 PHE E 244 TYR 0.009 0.001 TYR E 58 ARG 0.007 0.000 ARG A 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 20) link_NAG-ASN : angle 1.44011 ( 60) hydrogen bonds : bond 0.03635 ( 594) hydrogen bonds : angle 4.18065 ( 1947) SS BOND : bond 0.00096 ( 10) SS BOND : angle 0.59007 ( 20) covalent geometry : bond 0.00365 (12660) covalent geometry : angle 0.58194 (17300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7848 (tt0) cc_final: 0.7547 (mm-40) REVERT: D 173 GLN cc_start: 0.8045 (mt0) cc_final: 0.7539 (mm110) outliers start: 9 outliers final: 8 residues processed: 130 average time/residue: 2.2131 time to fit residues: 320.3152 Evaluate side-chains 134 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 64 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 26 optimal weight: 0.4980 chunk 51 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 ASN B 134 ASN B 173 GLN C 134 ASN E 173 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107236 restraints weight = 39716.573| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.24 r_work: 0.3216 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12690 Z= 0.121 Angle : 0.564 8.531 17380 Z= 0.282 Chirality : 0.041 0.142 2125 Planarity : 0.004 0.067 2020 Dihedral : 6.157 47.974 2480 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.66 % Allowed : 14.85 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.22), residues: 1450 helix: 3.58 (0.23), residues: 415 sheet: 0.27 (0.24), residues: 415 loop : -0.60 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 63 HIS 0.005 0.001 HIS D 128 PHE 0.017 0.001 PHE A 244 TYR 0.009 0.001 TYR B 75 ARG 0.009 0.000 ARG A 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 20) link_NAG-ASN : angle 1.32434 ( 60) hydrogen bonds : bond 0.03458 ( 594) hydrogen bonds : angle 4.11969 ( 1947) SS BOND : bond 0.00066 ( 10) SS BOND : angle 0.41200 ( 20) covalent geometry : bond 0.00286 (12660) covalent geometry : angle 0.55988 (17300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7587 (mm-40) REVERT: D 173 GLN cc_start: 0.7996 (mt0) cc_final: 0.7503 (mm110) outliers start: 9 outliers final: 6 residues processed: 135 average time/residue: 2.3135 time to fit residues: 351.5319 Evaluate side-chains 129 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 79 optimal weight: 0.0670 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN C 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107210 restraints weight = 39856.763| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.25 r_work: 0.3208 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12690 Z= 0.132 Angle : 0.569 9.297 17380 Z= 0.284 Chirality : 0.041 0.139 2125 Planarity : 0.004 0.054 2020 Dihedral : 6.047 47.057 2480 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.59 % Allowed : 15.07 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.22), residues: 1450 helix: 3.61 (0.23), residues: 415 sheet: 0.19 (0.23), residues: 435 loop : -0.51 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 63 HIS 0.005 0.001 HIS D 128 PHE 0.022 0.001 PHE A 244 TYR 0.009 0.001 TYR B 75 ARG 0.009 0.000 ARG A 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 20) link_NAG-ASN : angle 1.33969 ( 60) hydrogen bonds : bond 0.03444 ( 594) hydrogen bonds : angle 4.10328 ( 1947) SS BOND : bond 0.00081 ( 10) SS BOND : angle 0.55358 ( 20) covalent geometry : bond 0.00312 (12660) covalent geometry : angle 0.56480 (17300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7582 (mm-40) REVERT: D 173 GLN cc_start: 0.7991 (mt0) cc_final: 0.7491 (mm110) outliers start: 8 outliers final: 6 residues processed: 131 average time/residue: 2.3695 time to fit residues: 342.5922 Evaluate side-chains 132 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN C 134 ASN C 143 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.158993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106079 restraints weight = 39484.521| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.24 r_work: 0.3165 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12690 Z= 0.165 Angle : 0.600 10.151 17380 Z= 0.297 Chirality : 0.042 0.136 2125 Planarity : 0.004 0.058 2020 Dihedral : 6.178 47.883 2480 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.59 % Allowed : 15.15 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.22), residues: 1450 helix: 3.56 (0.23), residues: 415 sheet: 0.38 (0.25), residues: 390 loop : -0.63 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 118 HIS 0.005 0.002 HIS D 128 PHE 0.018 0.001 PHE A 244 TYR 0.009 0.001 TYR E 58 ARG 0.008 0.001 ARG A 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00099 ( 20) link_NAG-ASN : angle 1.39907 ( 60) hydrogen bonds : bond 0.03542 ( 594) hydrogen bonds : angle 4.12731 ( 1947) SS BOND : bond 0.00106 ( 10) SS BOND : angle 0.68350 ( 20) covalent geometry : bond 0.00394 (12660) covalent geometry : angle 0.59516 (17300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16427.53 seconds wall clock time: 278 minutes 16.17 seconds (16696.17 seconds total)