Starting phenix.real_space_refine on Sun Sep 13 00:50:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6sp2_10279/09_2026/6sp2_10279.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sp2_10279/09_2026/6sp2_10279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6sp2_10279/09_2026/6sp2_10279.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6sp2_10279/09_2026/6sp2_10279.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sp2_10279/09_2026/6sp2_10279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sp2_10279/09_2026/6sp2_10279.map" model { file = "/net/cci-nas-00/data/ceres_data/6sp2_10279/09_2026/6sp2_10279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sp2_10279/09_2026/6sp2_10279.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.136 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 P 18 5.49 5 S 156 5.16 5 C 12336 2.51 5 N 2640 2.21 5 O 3348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18498 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "B" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "C" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "D" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "E" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "F" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "A" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 3.78, per 1000 atoms: 0.20 Number of scatterers: 18498 At special positions: 0 Unit cell: (133.86, 144.9, 78.66, 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 156 16.00 P 18 15.00 O 3348 8.00 N 2640 7.00 C 12336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 238 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS B 238 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 95 " distance=2.04 Simple disulfide: pdb=" SG CYS C 238 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 238 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 238 " - pdb=" SG CYS E 299 " distance=2.03 Simple disulfide: pdb=" SG CYS F 71 " - pdb=" SG CYS F 95 " distance=2.04 Simple disulfide: pdb=" SG CYS F 238 " - pdb=" SG CYS F 299 " 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 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 738.1 milliseconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4080 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 75.0% alpha, 0.0% 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 30 through 55 removed outlier: 3.742A pdb=" N ASN A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'A' and resid 98 through 122 removed outlier: 4.213A pdb=" N MET A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 139 through 155 removed outlier: 3.718A pdb=" N LYS A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 201 removed outlier: 3.562A pdb=" N MET A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 201 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 232 removed outlier: 4.176A pdb=" N THR A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 259 removed outlier: 3.583A pdb=" N SER A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 256 " --> pdb=" O CYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.510A pdb=" N GLN A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 329 through 348 removed outlier: 3.507A pdb=" N ILE A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 416 removed outlier: 4.106A pdb=" N HIS A 401 " --> pdb=" O TRP A 397 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 416 " --> pdb=" O MET A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 454 removed outlier: 3.987A pdb=" N TRP A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 461 removed outlier: 3.811A pdb=" N VAL A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 55 removed outlier: 3.568A pdb=" N ALA B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 98 through 122 removed outlier: 4.214A pdb=" N MET B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 139 through 155 removed outlier: 3.717A pdb=" N LYS B 143 " --> pdb=" O PHE B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 201 removed outlier: 3.562A pdb=" N MET B 166 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 232 removed outlier: 4.175A pdb=" N THR B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 259 removed outlier: 3.584A pdb=" N SER B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 256 " --> pdb=" O CYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 268 removed outlier: 3.510A pdb=" N GLN B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 292 Processing helix chain 'B' and resid 329 through 348 removed outlier: 3.507A pdb=" N ILE B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 416 removed outlier: 4.107A pdb=" N HIS B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 416 " --> pdb=" O MET B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 454 removed outlier: 3.987A pdb=" N TRP B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 461 removed outlier: 3.812A pdb=" N VAL B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 55 removed outlier: 3.568A pdb=" N ALA C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 98 through 122 removed outlier: 4.213A pdb=" N MET C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 139 through 155 removed outlier: 3.718A pdb=" N LYS C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 201 removed outlier: 3.563A pdb=" N MET C 166 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 232 removed outlier: 4.176A pdb=" N THR C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 259 removed outlier: 3.584A pdb=" N SER C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER C 256 " --> pdb=" O CYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 268 removed outlier: 3.510A pdb=" N GLN C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG C 267 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 292 Processing helix chain 'C' and resid 329 through 348 removed outlier: 3.506A pdb=" N ILE C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 416 removed outlier: 4.106A pdb=" N HIS C 401 " --> pdb=" O TRP C 397 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR C 416 " --> pdb=" O MET C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 454 removed outlier: 3.987A pdb=" N TRP C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 461 removed outlier: 3.811A pdb=" N VAL C 458 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 55 removed outlier: 3.568A pdb=" N ALA D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 91 through 98 Processing helix chain 'D' and resid 98 through 122 removed outlier: 4.213A pdb=" N MET D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 139 through 155 removed outlier: 3.718A pdb=" N LYS D 143 " --> pdb=" O PHE D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 201 removed outlier: 3.563A pdb=" N MET D 166 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU D 201 " --> pdb=" O ILE D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 232 removed outlier: 4.176A pdb=" N THR D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 259 removed outlier: 3.584A pdb=" N SER D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER D 256 " --> pdb=" O CYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 266 removed outlier: 3.510A pdb=" N GLN D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 292 Processing helix chain 'D' and resid 329 through 348 removed outlier: 3.507A pdb=" N ILE D 333 " --> pdb=" O ASP D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 416 removed outlier: 4.107A pdb=" N HIS D 401 " --> pdb=" O TRP D 397 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR D 416 " --> pdb=" O MET D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 454 removed outlier: 3.987A pdb=" N TRP D 436 " --> pdb=" O GLU D 432 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 461 removed outlier: 3.811A pdb=" N VAL D 458 " --> pdb=" O ALA D 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 55 removed outlier: 3.568A pdb=" N ALA E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 68 Processing helix chain 'E' and resid 91 through 98 Processing helix chain 'E' and resid 98 through 122 removed outlier: 4.213A pdb=" N MET E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 139 through 155 removed outlier: 3.718A pdb=" N LYS E 143 " --> pdb=" O PHE E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 201 removed outlier: 3.562A pdb=" N MET E 166 " --> pdb=" O PHE E 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU E 201 " --> pdb=" O ILE E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 232 removed outlier: 4.176A pdb=" N THR E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 259 removed outlier: 3.583A pdb=" N SER E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER E 256 " --> pdb=" O CYS E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 268 removed outlier: 3.509A pdb=" N GLN E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG E 267 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 292 Processing helix chain 'E' and resid 329 through 348 removed outlier: 3.507A pdb=" N ILE E 333 " --> pdb=" O ASP E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 416 removed outlier: 4.106A pdb=" N HIS E 401 " --> pdb=" O TRP E 397 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR E 416 " --> pdb=" O MET E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 454 removed outlier: 3.987A pdb=" N TRP E 436 " --> pdb=" O GLU E 432 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 461 removed outlier: 3.811A pdb=" N VAL E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 55 removed outlier: 3.568A pdb=" N ALA F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 68 Processing helix chain 'F' and resid 91 through 98 Processing helix chain 'F' and resid 98 through 122 removed outlier: 4.214A pdb=" N MET F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 139 through 155 removed outlier: 3.717A pdb=" N LYS F 143 " --> pdb=" O PHE F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 201 removed outlier: 3.563A pdb=" N MET F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU F 201 " --> pdb=" O ILE F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 232 removed outlier: 4.176A pdb=" N THR F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 259 removed outlier: 3.584A pdb=" N SER F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER F 256 " --> pdb=" O CYS F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 268 removed outlier: 3.509A pdb=" N GLN F 265 " --> pdb=" O LEU F 261 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG F 267 " --> pdb=" O ALA F 263 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU F 268 " --> pdb=" O VAL F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 292 Processing helix chain 'F' and resid 329 through 348 removed outlier: 3.507A pdb=" N ILE F 333 " --> pdb=" O ASP F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 416 removed outlier: 4.106A pdb=" N HIS F 401 " --> pdb=" O TRP F 397 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR F 416 " --> pdb=" O MET F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 454 removed outlier: 3.987A pdb=" N TRP F 436 " --> pdb=" O GLU F 432 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 461 removed outlier: 3.812A pdb=" N VAL F 458 " --> pdb=" O ALA F 454 " (cutoff:3.500A) 1182 hydrogen bonds defined for protein. 3456 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: 2.72 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2692 1.32 - 1.45: 5412 1.45 - 1.58: 10586 1.58 - 1.70: 36 1.70 - 1.83: 234 Bond restraints: 18960 Sorted by residual: bond pdb=" OB3 CDL B1001 " pdb=" PB2 CDL B1001 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.51e+01 bond pdb=" OB3 CDL D1001 " pdb=" PB2 CDL D1001 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.51e+01 bond pdb=" OB3 CDL F1001 " pdb=" PB2 CDL F1001 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.50e+01 bond pdb=" OB3 CDL E1001 " pdb=" PB2 CDL E1001 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.46e+01 bond pdb=" OB3 CDL A 603 " pdb=" PB2 CDL A 603 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.00e-02 1.00e+04 2.44e+01 ... (remaining 18955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 24816 2.20 - 4.41: 701 4.41 - 6.61: 100 6.61 - 8.81: 15 8.81 - 11.01: 12 Bond angle restraints: 25644 Sorted by residual: angle pdb=" N PRO B 69 " pdb=" CA PRO B 69 " pdb=" C PRO B 69 " ideal model delta sigma weight residual 113.53 119.00 -5.47 1.39e+00 5.18e-01 1.55e+01 angle pdb=" N PRO E 69 " pdb=" CA PRO E 69 " pdb=" C PRO E 69 " ideal model delta sigma weight residual 113.53 118.99 -5.46 1.39e+00 5.18e-01 1.55e+01 angle pdb=" N VAL D 352 " pdb=" CA VAL D 352 " pdb=" C VAL D 352 " ideal model delta sigma weight residual 112.98 108.07 4.91 1.25e+00 6.40e-01 1.54e+01 angle pdb=" N PRO D 69 " pdb=" CA PRO D 69 " pdb=" C PRO D 69 " ideal model delta sigma weight residual 113.53 118.98 -5.45 1.39e+00 5.18e-01 1.54e+01 angle pdb=" N VAL F 352 " pdb=" CA VAL F 352 " pdb=" C VAL F 352 " ideal model delta sigma weight residual 112.98 108.08 4.90 1.25e+00 6.40e-01 1.54e+01 ... (remaining 25639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.24: 10374 26.24 - 52.48: 300 52.48 - 78.72: 102 78.72 - 104.96: 0 104.96 - 131.21: 24 Dihedral angle restraints: 10800 sinusoidal: 4452 harmonic: 6348 Sorted by residual: dihedral pdb=" CB CYS D 71 " pdb=" SG CYS D 71 " pdb=" SG CYS D 95 " pdb=" CB CYS D 95 " ideal model delta sinusoidal sigma weight residual 93.00 152.59 -59.59 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS F 71 " pdb=" SG CYS F 71 " pdb=" SG CYS F 95 " pdb=" CB CYS F 95 " ideal model delta sinusoidal sigma weight residual 93.00 152.58 -59.58 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS C 71 " pdb=" SG CYS C 71 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual 93.00 152.56 -59.56 1 1.00e+01 1.00e-02 4.74e+01 ... (remaining 10797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2370 0.052 - 0.105: 486 0.105 - 0.157: 118 0.157 - 0.209: 15 0.209 - 0.262: 11 Chirality restraints: 3000 Sorted by residual: chirality pdb=" C2 P5S D1004 " pdb=" C1 P5S D1004 " pdb=" C3 P5S D1004 " pdb=" O37 P5S D1004 " both_signs ideal model delta sigma weight residual False 2.32 2.58 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C2 P5S B1004 " pdb=" C1 P5S B1004 " pdb=" C3 P5S B1004 " pdb=" O37 P5S B1004 " both_signs ideal model delta sigma weight residual False 2.32 2.58 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C2 P5S C1004 " pdb=" C1 P5S C1004 " pdb=" C3 P5S C1004 " pdb=" O37 P5S C1004 " both_signs ideal model delta sigma weight residual False 2.32 2.58 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2997 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 268 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO F 269 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 269 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 269 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 268 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO B 269 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 269 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 269 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 268 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO A 269 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.023 5.00e-02 4.00e+02 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 6 2.25 - 2.91: 7574 2.91 - 3.58: 26348 3.58 - 4.24: 38831 4.24 - 4.90: 68058 Nonbonded interactions: 140817 Sorted by model distance: nonbonded pdb=" O3 LMN F1002 " pdb=" OAU LMN F1002 " model vdw 1.590 3.040 nonbonded pdb=" O3 LMN A 604 " pdb=" OAU LMN A 604 " model vdw 1.590 3.040 nonbonded pdb=" O3 LMN D1002 " pdb=" OAU LMN D1002 " model vdw 1.590 3.040 nonbonded pdb=" O3 LMN E1002 " pdb=" OAU LMN E1002 " model vdw 1.590 3.040 nonbonded pdb=" O3 LMN B1002 " pdb=" OAU LMN B1002 " model vdw 1.590 3.040 ... (remaining 140812 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 30 through 461) selection = (chain 'B' and resid 30 through 461) selection = (chain 'C' and resid 30 through 461) selection = (chain 'D' and resid 30 through 461) selection = (chain 'E' and resid 30 through 461) selection = (chain 'F' and resid 30 through 461) } 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.820 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.020 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 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 : 0.006 0.056 18972 Z= 0.291 Angle : 0.852 11.015 25668 Z= 0.431 Chirality : 0.049 0.262 3000 Planarity : 0.005 0.041 2904 Dihedral : 15.172 131.205 6684 Min Nonbonded Distance : 1.590 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: -0.56 (0.17), residues: 2142 helix: 0.38 (0.12), residues: 1434 sheet: None (None), residues: 0 loop : -1.86 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 106 TYR 0.019 0.002 TYR E 419 PHE 0.022 0.002 PHE F 404 TRP 0.025 0.003 TRP E 418 HIS 0.007 0.002 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.29 (18960) covalent geometry : angle 0.84912 / 0.43 (25644) SS BOND : bond 0.00690 / 0.40 ( 12) SS BOND : angle 2.51383 / 1.50 ( 24) hydrogen bonds : bond 0.12815 / 8.67 ( 1182) hydrogen bonds : angle 4.43918 / 3.22 ( 3456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.663 Fit side-chains REVERT: A 122 MET cc_start: 0.7416 (mmt) cc_final: 0.6781 (mmt) REVERT: A 166 MET cc_start: 0.7177 (mmm) cc_final: 0.6593 (mmt) REVERT: A 204 ARG cc_start: 0.7555 (mtp180) cc_final: 0.7216 (ttt-90) REVERT: A 271 SER cc_start: 0.8203 (t) cc_final: 0.7910 (t) REVERT: B 102 MET cc_start: 0.7053 (mtm) cc_final: 0.6456 (mtp) REVERT: B 122 MET cc_start: 0.7520 (mmt) cc_final: 0.6983 (mmt) REVERT: B 297 LYS cc_start: 0.9076 (ptmm) cc_final: 0.8721 (tttp) REVERT: B 298 GLU cc_start: 0.8257 (tp30) cc_final: 0.7959 (tp30) REVERT: C 102 MET cc_start: 0.6711 (mtm) cc_final: 0.6242 (mtp) REVERT: C 122 MET cc_start: 0.7250 (mmt) cc_final: 0.6942 (mmt) REVERT: C 271 SER cc_start: 0.8511 (t) cc_final: 0.8282 (t) REVERT: C 297 LYS cc_start: 0.8978 (ptmm) cc_final: 0.8644 (tttp) REVERT: C 298 GLU cc_start: 0.8265 (tp30) cc_final: 0.8056 (tp30) REVERT: D 122 MET cc_start: 0.7347 (mmt) cc_final: 0.6704 (mmt) REVERT: D 166 MET cc_start: 0.7217 (mmm) cc_final: 0.6623 (mmt) REVERT: D 204 ARG cc_start: 0.7674 (mtp180) cc_final: 0.7388 (ttt-90) REVERT: D 271 SER cc_start: 0.8245 (t) cc_final: 0.7947 (t) REVERT: E 102 MET cc_start: 0.7027 (mtm) cc_final: 0.6372 (mtp) REVERT: E 122 MET cc_start: 0.7538 (mmt) cc_final: 0.7021 (mmt) REVERT: E 297 LYS cc_start: 0.9089 (ptmm) cc_final: 0.8697 (tttp) REVERT: F 122 MET cc_start: 0.7240 (mmt) cc_final: 0.6956 (mmt) REVERT: F 271 SER cc_start: 0.8010 (t) cc_final: 0.7740 (t) REVERT: F 297 LYS cc_start: 0.8989 (ptmm) cc_final: 0.8640 (tttp) REVERT: F 298 GLU cc_start: 0.8287 (tp30) cc_final: 0.8077 (tp30) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.1353 time to fit residues: 64.9240 Evaluate side-chains 218 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 181 GLN A 422 HIS B 136 GLN B 181 GLN B 422 HIS C 136 GLN C 181 GLN C 422 HIS D 181 GLN D 422 HIS E 136 GLN E 181 GLN E 332 ASN E 422 HIS F 136 GLN F 181 GLN F 422 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.155430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114109 restraints weight = 23247.786| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.71 r_work: 0.3364 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18972 Z= 0.151 Angle : 0.669 12.111 25668 Z= 0.312 Chirality : 0.042 0.161 3000 Planarity : 0.004 0.034 2904 Dihedral : 16.526 160.991 3078 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.98 % Allowed : 8.33 % Favored : 89.69 % 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: 1.04 (0.18), residues: 2142 helix: 1.69 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.71 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 39 TYR 0.012 0.001 TYR A 419 PHE 0.010 0.001 PHE A 177 TRP 0.015 0.002 TRP B 288 HIS 0.003 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (18960) covalent geometry : angle 0.66765 / 0.31 (25644) SS BOND : bond 0.00239 / 0.14 ( 12) SS BOND : angle 1.33170 / 0.77 ( 24) hydrogen bonds : bond 0.05715 / 3.75 ( 1182) hydrogen bonds : angle 3.39175 / 2.43 ( 3456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.711 Fit side-chains REVERT: A 122 MET cc_start: 0.8102 (mmt) cc_final: 0.7483 (mmt) REVERT: A 166 MET cc_start: 0.8060 (mmm) cc_final: 0.7652 (mmt) REVERT: A 271 SER cc_start: 0.8838 (t) cc_final: 0.8534 (t) REVERT: A 413 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.7580 (mpp) REVERT: A 435 MET cc_start: 0.7776 (ptm) cc_final: 0.7570 (ptt) REVERT: B 102 MET cc_start: 0.8116 (mtm) cc_final: 0.7744 (mtp) REVERT: B 122 MET cc_start: 0.8293 (mmt) cc_final: 0.7696 (mmt) REVERT: B 303 MET cc_start: 0.6193 (mmm) cc_final: 0.5269 (mmt) REVERT: C 122 MET cc_start: 0.7855 (mmt) cc_final: 0.7347 (mmt) REVERT: C 129 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.7813 (mtm-85) REVERT: C 204 ARG cc_start: 0.8198 (tpt170) cc_final: 0.7375 (ttt180) REVERT: C 297 LYS cc_start: 0.9022 (ptmm) cc_final: 0.8805 (tttp) REVERT: D 122 MET cc_start: 0.8050 (mmt) cc_final: 0.7449 (mmt) REVERT: D 166 MET cc_start: 0.8080 (mmm) cc_final: 0.7652 (mmt) REVERT: D 271 SER cc_start: 0.8820 (t) cc_final: 0.8516 (t) REVERT: E 102 MET cc_start: 0.8127 (mtm) cc_final: 0.7717 (mtp) REVERT: E 122 MET cc_start: 0.8228 (mmt) cc_final: 0.7648 (mmt) REVERT: E 303 MET cc_start: 0.6185 (mmm) cc_final: 0.5308 (mmt) REVERT: F 122 MET cc_start: 0.7902 (mmt) cc_final: 0.7436 (mmt) REVERT: F 129 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.7843 (mtm-85) REVERT: F 204 ARG cc_start: 0.8125 (tpt170) cc_final: 0.7374 (ttt180) REVERT: F 297 LYS cc_start: 0.9040 (ptmm) cc_final: 0.8837 (tttp) outliers start: 37 outliers final: 33 residues processed: 238 average time/residue: 0.1421 time to fit residues: 51.7661 Evaluate side-chains 230 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 136 GLN E 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.154440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.112863 restraints weight = 23650.343| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.72 r_work: 0.3346 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18972 Z= 0.143 Angle : 0.621 11.767 25668 Z= 0.295 Chirality : 0.041 0.148 3000 Planarity : 0.004 0.033 2904 Dihedral : 14.967 154.921 3078 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.04 % Allowed : 10.79 % Favored : 86.16 % 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: 1.64 (0.19), residues: 2142 helix: 2.14 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.47 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 39 TYR 0.011 0.001 TYR A 419 PHE 0.010 0.001 PHE D 177 TRP 0.012 0.001 TRP B 288 HIS 0.002 0.001 HIS C 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (18960) covalent geometry : angle 0.62083 / 0.29 (25644) SS BOND : bond 0.00208 / 0.11 ( 12) SS BOND : angle 1.06432 / 0.61 ( 24) hydrogen bonds : bond 0.05552 / 3.65 ( 1182) hydrogen bonds : angle 3.24802 / 2.32 ( 3456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 203 time to evaluate : 0.612 Fit side-chains REVERT: A 122 MET cc_start: 0.8102 (mmt) cc_final: 0.7671 (tpp) REVERT: A 166 MET cc_start: 0.8289 (mmm) cc_final: 0.7758 (mmt) REVERT: A 271 SER cc_start: 0.8858 (t) cc_final: 0.8538 (t) REVERT: B 122 MET cc_start: 0.8237 (mmt) cc_final: 0.7662 (mmt) REVERT: B 166 MET cc_start: 0.8087 (mmm) cc_final: 0.7831 (mmp) REVERT: B 204 ARG cc_start: 0.8242 (ttt180) cc_final: 0.7541 (tpt170) REVERT: C 122 MET cc_start: 0.7886 (mmt) cc_final: 0.7453 (mmt) REVERT: C 129 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.7830 (mtm-85) REVERT: C 204 ARG cc_start: 0.8262 (tpt170) cc_final: 0.7476 (ttt180) REVERT: C 297 LYS cc_start: 0.9041 (ptmm) cc_final: 0.8827 (tttp) REVERT: C 303 MET cc_start: 0.7452 (mpp) cc_final: 0.6833 (mtm) REVERT: D 122 MET cc_start: 0.8065 (mmt) cc_final: 0.7505 (mmt) REVERT: D 166 MET cc_start: 0.8298 (mmm) cc_final: 0.7763 (mmt) REVERT: D 271 SER cc_start: 0.8819 (t) cc_final: 0.8526 (t) REVERT: E 122 MET cc_start: 0.8218 (mmt) cc_final: 0.7662 (mmt) REVERT: E 166 MET cc_start: 0.7898 (mmt) cc_final: 0.7652 (mmt) REVERT: F 122 MET cc_start: 0.7891 (mmt) cc_final: 0.7469 (mmt) REVERT: F 129 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.7812 (mtm-85) REVERT: F 204 ARG cc_start: 0.8185 (tpt170) cc_final: 0.7445 (ttt180) REVERT: F 297 LYS cc_start: 0.9075 (ptmm) cc_final: 0.8863 (tttp) REVERT: F 303 MET cc_start: 0.7568 (mpp) cc_final: 0.6779 (mtm) outliers start: 57 outliers final: 47 residues processed: 235 average time/residue: 0.1381 time to fit residues: 49.6926 Evaluate side-chains 247 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 175 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 201 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.155652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113574 restraints weight = 23570.633| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.76 r_work: 0.3360 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18972 Z= 0.133 Angle : 0.611 11.518 25668 Z= 0.286 Chirality : 0.041 0.144 3000 Planarity : 0.003 0.033 2904 Dihedral : 13.498 138.394 3078 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.47 % Allowed : 10.84 % Favored : 85.68 % 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: 1.91 (0.19), residues: 2142 helix: 2.38 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.45 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.010 0.001 TYR D 419 PHE 0.009 0.001 PHE C 177 TRP 0.008 0.001 TRP E 288 HIS 0.002 0.000 HIS C 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (18960) covalent geometry : angle 0.60949 / 0.29 (25644) SS BOND : bond 0.00215 / 0.12 ( 12) SS BOND : angle 1.32367 / 0.76 ( 24) hydrogen bonds : bond 0.05182 / 3.41 ( 1182) hydrogen bonds : angle 3.15148 / 2.25 ( 3456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 0.666 Fit side-chains REVERT: A 122 MET cc_start: 0.7982 (mmt) cc_final: 0.7608 (tpp) REVERT: A 166 MET cc_start: 0.8305 (mmm) cc_final: 0.7832 (mmt) REVERT: A 271 SER cc_start: 0.8878 (t) cc_final: 0.8591 (t) REVERT: B 122 MET cc_start: 0.7995 (mmt) cc_final: 0.7412 (mmt) REVERT: B 166 MET cc_start: 0.8096 (mmm) cc_final: 0.7770 (mmp) REVERT: B 261 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7724 (pp) REVERT: C 122 MET cc_start: 0.7794 (mmt) cc_final: 0.7350 (mmt) REVERT: C 129 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.7819 (mtm-85) REVERT: C 204 ARG cc_start: 0.8336 (tpt170) cc_final: 0.7538 (ttt180) REVERT: C 261 LEU cc_start: 0.7789 (pp) cc_final: 0.7513 (pp) REVERT: C 303 MET cc_start: 0.7436 (mpp) cc_final: 0.6819 (mtm) REVERT: D 122 MET cc_start: 0.7976 (mmt) cc_final: 0.7594 (tpp) REVERT: D 166 MET cc_start: 0.8300 (mmm) cc_final: 0.7835 (mmt) REVERT: D 271 SER cc_start: 0.8886 (t) cc_final: 0.8586 (t) REVERT: E 122 MET cc_start: 0.8069 (mmt) cc_final: 0.7498 (mmt) REVERT: E 166 MET cc_start: 0.8011 (mmt) cc_final: 0.7760 (mmt) REVERT: F 122 MET cc_start: 0.7776 (mmt) cc_final: 0.7359 (mmt) REVERT: F 129 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.7808 (mtm-85) REVERT: F 204 ARG cc_start: 0.8203 (tpt170) cc_final: 0.7452 (ttt180) REVERT: F 303 MET cc_start: 0.7492 (mpp) cc_final: 0.6861 (mtm) outliers start: 65 outliers final: 49 residues processed: 249 average time/residue: 0.1312 time to fit residues: 50.7008 Evaluate side-chains 250 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 419 TYR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 58 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 chunk 183 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.156003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.114087 restraints weight = 23505.347| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.74 r_work: 0.3369 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18972 Z= 0.125 Angle : 0.590 11.276 25668 Z= 0.275 Chirality : 0.040 0.157 3000 Planarity : 0.003 0.035 2904 Dihedral : 12.582 131.958 3078 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.49 % Allowed : 10.10 % Favored : 85.42 % 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: 2.08 (0.19), residues: 2142 helix: 2.56 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.54 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.008 0.001 TYR A 419 PHE 0.010 0.001 PHE D 177 TRP 0.007 0.001 TRP F 140 HIS 0.002 0.000 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (18960) covalent geometry : angle 0.58889 / 0.27 (25644) SS BOND : bond 0.00227 / 0.13 ( 12) SS BOND : angle 1.26846 / 0.74 ( 24) hydrogen bonds : bond 0.04967 / 3.26 ( 1182) hydrogen bonds : angle 3.06697 / 2.19 ( 3456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 209 time to evaluate : 0.655 Fit side-chains REVERT: A 122 MET cc_start: 0.7906 (mmt) cc_final: 0.7554 (tpp) REVERT: A 155 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.8010 (mt) REVERT: A 166 MET cc_start: 0.8253 (mmm) cc_final: 0.7777 (mmt) REVERT: A 190 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.6512 (m-70) REVERT: A 229 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7126 (t80) REVERT: A 261 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7140 (pp) REVERT: A 271 SER cc_start: 0.8844 (t) cc_final: 0.8544 (t) REVERT: B 122 MET cc_start: 0.7887 (mmt) cc_final: 0.7351 (mmt) REVERT: B 166 MET cc_start: 0.8092 (mmm) cc_final: 0.7750 (mmp) REVERT: B 204 ARG cc_start: 0.8251 (ttt180) cc_final: 0.7578 (tpt170) REVERT: B 258 ILE cc_start: 0.7918 (tt) cc_final: 0.7619 (tt) REVERT: C 122 MET cc_start: 0.7809 (mmt) cc_final: 0.7307 (mmt) REVERT: C 129 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.7796 (mtm-85) REVERT: C 155 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7876 (tt) REVERT: C 204 ARG cc_start: 0.8265 (tpt170) cc_final: 0.7429 (ttt180) REVERT: C 303 MET cc_start: 0.7471 (mpp) cc_final: 0.6912 (mtm) REVERT: D 122 MET cc_start: 0.7906 (mmt) cc_final: 0.7547 (tpp) REVERT: D 129 ARG cc_start: 0.8354 (mmm-85) cc_final: 0.7980 (mtm-85) REVERT: D 155 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.8007 (mt) REVERT: D 166 MET cc_start: 0.8259 (mmm) cc_final: 0.7788 (mmt) REVERT: D 190 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.6509 (m-70) REVERT: D 229 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7100 (t80) REVERT: D 271 SER cc_start: 0.8864 (t) cc_final: 0.8558 (t) REVERT: E 122 MET cc_start: 0.7875 (mmt) cc_final: 0.7352 (mmt) REVERT: E 166 MET cc_start: 0.8043 (mmt) cc_final: 0.7818 (mmt) REVERT: E 258 ILE cc_start: 0.7957 (tt) cc_final: 0.7677 (tt) REVERT: E 261 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7627 (pp) REVERT: E 268 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7747 (pp) REVERT: F 122 MET cc_start: 0.7794 (mmt) cc_final: 0.7312 (mmt) REVERT: F 129 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.7755 (mtm-85) REVERT: F 155 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7881 (tt) REVERT: F 204 ARG cc_start: 0.8218 (tpt170) cc_final: 0.7407 (ttt180) REVERT: F 303 MET cc_start: 0.7419 (mpp) cc_final: 0.6847 (mtm) outliers start: 84 outliers final: 59 residues processed: 272 average time/residue: 0.1389 time to fit residues: 58.6518 Evaluate side-chains 279 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 209 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 229 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 419 TYR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 25 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 206 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.154933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.113012 restraints weight = 23439.299| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.76 r_work: 0.3356 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18972 Z= 0.129 Angle : 0.594 11.281 25668 Z= 0.278 Chirality : 0.040 0.159 3000 Planarity : 0.003 0.035 2904 Dihedral : 11.993 123.683 3078 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.43 % Allowed : 10.58 % Favored : 84.99 % 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: 2.16 (0.19), residues: 2142 helix: 2.64 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.56 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.010 0.001 TYR A 419 PHE 0.010 0.001 PHE D 177 TRP 0.007 0.001 TRP E 288 HIS 0.002 0.000 HIS D 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (18960) covalent geometry : angle 0.59306 / 0.28 (25644) SS BOND : bond 0.00229 / 0.13 ( 12) SS BOND : angle 1.02502 / 0.59 ( 24) hydrogen bonds : bond 0.05117 / 3.36 ( 1182) hydrogen bonds : angle 3.06864 / 2.19 ( 3456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 208 time to evaluate : 0.571 Fit side-chains REVERT: A 122 MET cc_start: 0.7974 (mmt) cc_final: 0.7607 (tpp) REVERT: A 129 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.7938 (mtm-85) REVERT: A 166 MET cc_start: 0.8334 (mmm) cc_final: 0.7826 (mmt) REVERT: A 190 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.6509 (m-70) REVERT: A 229 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7360 (t80) REVERT: A 258 ILE cc_start: 0.8049 (tt) cc_final: 0.7840 (tt) REVERT: A 261 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7168 (pp) REVERT: B 122 MET cc_start: 0.7969 (mmt) cc_final: 0.7460 (mmt) REVERT: B 155 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8114 (tt) REVERT: B 166 MET cc_start: 0.8150 (mmm) cc_final: 0.7807 (mmp) REVERT: B 204 ARG cc_start: 0.8246 (ttt180) cc_final: 0.7523 (tpt170) REVERT: B 258 ILE cc_start: 0.7984 (tt) cc_final: 0.7705 (tt) REVERT: B 261 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7724 (pp) REVERT: B 268 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7678 (pp) REVERT: C 122 MET cc_start: 0.7878 (mmt) cc_final: 0.7424 (mmt) REVERT: C 129 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.7741 (mtm-85) REVERT: C 155 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7889 (tt) REVERT: C 204 ARG cc_start: 0.8245 (tpt170) cc_final: 0.7361 (ttt180) REVERT: C 303 MET cc_start: 0.7503 (mpp) cc_final: 0.6998 (mtm) REVERT: D 122 MET cc_start: 0.7976 (mmt) cc_final: 0.7606 (tpp) REVERT: D 129 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7944 (mtm-85) REVERT: D 166 MET cc_start: 0.8338 (mmm) cc_final: 0.7825 (mmt) REVERT: D 190 HIS cc_start: 0.7950 (OUTLIER) cc_final: 0.6510 (m-70) REVERT: D 229 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7266 (t80) REVERT: D 271 SER cc_start: 0.8921 (t) cc_final: 0.8590 (t) REVERT: E 122 MET cc_start: 0.7965 (mmt) cc_final: 0.7476 (mmt) REVERT: E 155 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8126 (tt) REVERT: E 258 ILE cc_start: 0.8017 (tt) cc_final: 0.7729 (tt) REVERT: E 261 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7693 (pp) REVERT: E 268 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7751 (pp) REVERT: F 122 MET cc_start: 0.7790 (mmt) cc_final: 0.7326 (mmt) REVERT: F 129 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.7740 (mtm-85) REVERT: F 204 ARG cc_start: 0.8237 (tpt170) cc_final: 0.7414 (ttt180) REVERT: F 303 MET cc_start: 0.7453 (mpp) cc_final: 0.6937 (mtm) outliers start: 83 outliers final: 61 residues processed: 270 average time/residue: 0.1326 time to fit residues: 55.1747 Evaluate side-chains 280 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 207 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 229 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 419 TYR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 185 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 195 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.153967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112470 restraints weight = 23747.386| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.74 r_work: 0.3357 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18972 Z= 0.132 Angle : 0.599 11.270 25668 Z= 0.280 Chirality : 0.040 0.162 3000 Planarity : 0.003 0.035 2904 Dihedral : 11.561 113.603 3078 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.54 % Allowed : 11.11 % Favored : 84.35 % 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: 2.23 (0.19), residues: 2142 helix: 2.71 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.57 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.010 0.001 TYR A 419 PHE 0.010 0.001 PHE D 177 TRP 0.007 0.001 TRP E 288 HIS 0.002 0.000 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (18960) covalent geometry : angle 0.59865 / 0.28 (25644) SS BOND : bond 0.00229 / 0.13 ( 12) SS BOND : angle 0.95575 / 0.55 ( 24) hydrogen bonds : bond 0.05163 / 3.39 ( 1182) hydrogen bonds : angle 3.06682 / 2.19 ( 3456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 212 time to evaluate : 0.679 Fit side-chains REVERT: A 68 MET cc_start: 0.7960 (mmp) cc_final: 0.7590 (mmt) REVERT: A 122 MET cc_start: 0.8043 (mmt) cc_final: 0.7623 (tpp) REVERT: A 129 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.7930 (mtm-85) REVERT: A 155 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8081 (mt) REVERT: A 190 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.6528 (m-70) REVERT: A 229 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7381 (t80) REVERT: A 258 ILE cc_start: 0.8087 (tt) cc_final: 0.7866 (tt) REVERT: A 261 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7234 (pp) REVERT: B 122 MET cc_start: 0.7994 (mmt) cc_final: 0.7485 (mmt) REVERT: B 155 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8121 (tt) REVERT: B 166 MET cc_start: 0.8150 (mmm) cc_final: 0.7805 (mmp) REVERT: B 204 ARG cc_start: 0.8271 (ttt180) cc_final: 0.7571 (tpt170) REVERT: B 258 ILE cc_start: 0.7994 (tt) cc_final: 0.7757 (tt) REVERT: B 261 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7770 (pp) REVERT: B 268 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7619 (pp) REVERT: C 122 MET cc_start: 0.7838 (mmt) cc_final: 0.7350 (mmt) REVERT: C 129 ARG cc_start: 0.8242 (mmm-85) cc_final: 0.7756 (mtm-85) REVERT: C 155 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7902 (tt) REVERT: C 204 ARG cc_start: 0.8190 (tpt170) cc_final: 0.7225 (ttt180) REVERT: C 303 MET cc_start: 0.7533 (mpp) cc_final: 0.7043 (mtm) REVERT: D 122 MET cc_start: 0.8007 (mmt) cc_final: 0.7616 (tpp) REVERT: D 129 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.7944 (mtm-85) REVERT: D 155 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.8018 (mt) REVERT: D 190 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.6616 (m-70) REVERT: D 229 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7411 (t80) REVERT: E 122 MET cc_start: 0.7982 (mmt) cc_final: 0.7469 (mmt) REVERT: E 155 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8140 (tt) REVERT: E 206 TYR cc_start: 0.5964 (m-10) cc_final: 0.5607 (m-10) REVERT: E 258 ILE cc_start: 0.8060 (tt) cc_final: 0.7754 (tt) REVERT: E 261 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7727 (pp) REVERT: E 268 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7801 (pp) REVERT: F 122 MET cc_start: 0.7827 (mmt) cc_final: 0.7348 (mmt) REVERT: F 129 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.7763 (mtm-85) REVERT: F 155 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7910 (tt) REVERT: F 204 ARG cc_start: 0.8255 (tpt170) cc_final: 0.7785 (ttt90) REVERT: F 303 MET cc_start: 0.7513 (mpp) cc_final: 0.7052 (mtm) outliers start: 85 outliers final: 67 residues processed: 271 average time/residue: 0.1339 time to fit residues: 56.1851 Evaluate side-chains 286 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 204 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 229 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 419 TYR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 200 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 165 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 141 optimal weight: 0.0570 chunk 109 optimal weight: 2.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN F 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.157846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116014 restraints weight = 23302.215| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.74 r_work: 0.3399 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18972 Z= 0.112 Angle : 0.577 10.875 25668 Z= 0.267 Chirality : 0.039 0.159 3000 Planarity : 0.003 0.034 2904 Dihedral : 11.027 104.344 3078 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.38 % Allowed : 11.49 % Favored : 84.13 % 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: 2.60 (0.19), residues: 2142 helix: 3.02 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.006 0.001 TYR D 419 PHE 0.009 0.001 PHE D 177 TRP 0.005 0.001 TRP F 140 HIS 0.002 0.000 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (18960) covalent geometry : angle 0.57632 / 0.27 (25644) SS BOND : bond 0.00204 / 0.12 ( 12) SS BOND : angle 0.79083 / 0.45 ( 24) hydrogen bonds : bond 0.04435 / 2.91 ( 1182) hydrogen bonds : angle 2.92886 / 2.09 ( 3456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 227 time to evaluate : 0.589 Fit side-chains REVERT: A 122 MET cc_start: 0.7731 (mmt) cc_final: 0.7413 (tpp) REVERT: A 129 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.7935 (mtm-85) REVERT: A 190 HIS cc_start: 0.7864 (OUTLIER) cc_final: 0.6615 (m-70) REVERT: A 229 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7379 (t80) REVERT: A 258 ILE cc_start: 0.8038 (tt) cc_final: 0.7825 (tt) REVERT: A 261 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7067 (pp) REVERT: A 413 MET cc_start: 0.8638 (tpp) cc_final: 0.8405 (mmm) REVERT: B 122 MET cc_start: 0.7678 (mmt) cc_final: 0.7373 (mmt) REVERT: B 155 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.8035 (tt) REVERT: B 166 MET cc_start: 0.7995 (mmm) cc_final: 0.7662 (mmp) REVERT: B 204 ARG cc_start: 0.8162 (ttt180) cc_final: 0.7428 (tpt170) REVERT: B 258 ILE cc_start: 0.7881 (tt) cc_final: 0.7580 (tt) REVERT: B 261 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7617 (pp) REVERT: B 268 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7520 (pp) REVERT: B 270 HIS cc_start: 0.7316 (p-80) cc_final: 0.7089 (p-80) REVERT: C 122 MET cc_start: 0.7485 (mmt) cc_final: 0.7008 (mmt) REVERT: C 129 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7793 (mtm-85) REVERT: C 155 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7807 (tt) REVERT: C 204 ARG cc_start: 0.8150 (tpt170) cc_final: 0.7570 (ttt90) REVERT: C 303 MET cc_start: 0.7474 (mpp) cc_final: 0.7038 (mtm) REVERT: D 122 MET cc_start: 0.7726 (mmt) cc_final: 0.7401 (tpp) REVERT: D 129 ARG cc_start: 0.8347 (mmm-85) cc_final: 0.7927 (mtm-85) REVERT: D 155 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7938 (mt) REVERT: D 190 HIS cc_start: 0.7862 (OUTLIER) cc_final: 0.6619 (m-70) REVERT: D 229 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7414 (t80) REVERT: D 258 ILE cc_start: 0.8046 (tt) cc_final: 0.7800 (tt) REVERT: D 413 MET cc_start: 0.8645 (tpp) cc_final: 0.8411 (mmm) REVERT: E 122 MET cc_start: 0.7675 (mmt) cc_final: 0.7363 (mmt) REVERT: E 155 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.8049 (tt) REVERT: E 206 TYR cc_start: 0.5894 (m-10) cc_final: 0.5606 (m-10) REVERT: E 258 ILE cc_start: 0.7965 (tt) cc_final: 0.7675 (tt) REVERT: E 261 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7538 (pp) REVERT: E 268 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7610 (pp) REVERT: E 270 HIS cc_start: 0.7319 (p-80) cc_final: 0.7100 (p-80) REVERT: F 122 MET cc_start: 0.7469 (mmt) cc_final: 0.7197 (mmt) REVERT: F 129 ARG cc_start: 0.8291 (mmm-85) cc_final: 0.7805 (mtm-85) REVERT: F 155 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7802 (tt) REVERT: F 204 ARG cc_start: 0.8230 (tpt170) cc_final: 0.7774 (ttt90) REVERT: F 303 MET cc_start: 0.7461 (mpp) cc_final: 0.6997 (mtm) outliers start: 82 outliers final: 58 residues processed: 283 average time/residue: 0.1318 time to fit residues: 58.3114 Evaluate side-chains 286 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 214 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 229 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 419 TYR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 8 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 112 optimal weight: 0.0270 chunk 190 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 429 ASN F 429 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.156249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114578 restraints weight = 23605.275| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.75 r_work: 0.3371 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18972 Z= 0.121 Angle : 0.590 11.222 25668 Z= 0.274 Chirality : 0.039 0.168 3000 Planarity : 0.003 0.035 2904 Dihedral : 10.951 99.786 3078 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.06 % Allowed : 12.61 % Favored : 83.33 % 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: 2.61 (0.19), residues: 2142 helix: 3.04 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.30 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.009 0.001 TYR D 419 PHE 0.010 0.001 PHE A 177 TRP 0.006 0.001 TRP E 288 HIS 0.002 0.000 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (18960) covalent geometry : angle 0.58972 / 0.27 (25644) SS BOND : bond 0.00181 / 0.10 ( 12) SS BOND : angle 0.77766 / 0.44 ( 24) hydrogen bonds : bond 0.04788 / 3.14 ( 1182) hydrogen bonds : angle 2.96271 / 2.11 ( 3456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 212 time to evaluate : 0.645 Fit side-chains REVERT: A 122 MET cc_start: 0.7825 (mmt) cc_final: 0.7511 (tpp) REVERT: A 129 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.7940 (mtm-85) REVERT: A 190 HIS cc_start: 0.7856 (OUTLIER) cc_final: 0.6585 (m-70) REVERT: A 206 TYR cc_start: 0.6210 (m-10) cc_final: 0.5841 (m-10) REVERT: A 229 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7401 (t80) REVERT: A 258 ILE cc_start: 0.8052 (tt) cc_final: 0.7837 (tt) REVERT: A 261 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7083 (pp) REVERT: B 122 MET cc_start: 0.7848 (mmt) cc_final: 0.7547 (mmt) REVERT: B 155 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.8050 (tt) REVERT: B 166 MET cc_start: 0.8085 (mmm) cc_final: 0.7734 (mmp) REVERT: B 204 ARG cc_start: 0.8140 (ttt180) cc_final: 0.7414 (tpt170) REVERT: B 258 ILE cc_start: 0.7999 (tt) cc_final: 0.7694 (tt) REVERT: B 261 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7660 (pp) REVERT: B 268 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7527 (pp) REVERT: B 270 HIS cc_start: 0.7331 (p-80) cc_final: 0.7105 (p-80) REVERT: C 122 MET cc_start: 0.7561 (mmt) cc_final: 0.7063 (mmt) REVERT: C 129 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.7799 (mtm-85) REVERT: C 155 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7807 (tt) REVERT: C 204 ARG cc_start: 0.8143 (tpt170) cc_final: 0.7580 (ttt90) REVERT: D 122 MET cc_start: 0.7826 (mmt) cc_final: 0.7496 (tpp) REVERT: D 129 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.7929 (mtm-85) REVERT: D 155 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7938 (mt) REVERT: D 190 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.6606 (m-70) REVERT: D 229 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7388 (t80) REVERT: D 258 ILE cc_start: 0.8056 (tt) cc_final: 0.7802 (tt) REVERT: E 122 MET cc_start: 0.7854 (mmt) cc_final: 0.7544 (mmt) REVERT: E 155 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8062 (tt) REVERT: E 206 TYR cc_start: 0.5983 (m-10) cc_final: 0.5715 (m-10) REVERT: E 258 ILE cc_start: 0.8004 (tt) cc_final: 0.7705 (tt) REVERT: E 261 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7431 (pp) REVERT: E 268 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7712 (pp) REVERT: E 270 HIS cc_start: 0.7346 (p-80) cc_final: 0.7126 (p-80) REVERT: F 122 MET cc_start: 0.7664 (mmt) cc_final: 0.7334 (mmt) REVERT: F 129 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.7742 (mtm-85) REVERT: F 155 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7814 (tt) REVERT: F 204 ARG cc_start: 0.8228 (tpt170) cc_final: 0.7781 (ttt90) REVERT: F 258 ILE cc_start: 0.8128 (tt) cc_final: 0.7841 (tt) REVERT: F 303 MET cc_start: 0.7484 (mpp) cc_final: 0.7100 (mtm) outliers start: 76 outliers final: 57 residues processed: 266 average time/residue: 0.1351 time to fit residues: 55.6378 Evaluate side-chains 282 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 211 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 229 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 419 TYR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 180 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.153672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.112182 restraints weight = 23607.493| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.74 r_work: 0.3340 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18972 Z= 0.140 Angle : 0.613 11.414 25668 Z= 0.287 Chirality : 0.040 0.155 3000 Planarity : 0.003 0.036 2904 Dihedral : 11.093 97.007 3078 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.01 % Allowed : 12.61 % Favored : 83.39 % 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: 2.35 (0.19), residues: 2142 helix: 2.80 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.012 0.001 TYR D 419 PHE 0.010 0.001 PHE D 177 TRP 0.009 0.001 TRP B 288 HIS 0.002 0.000 HIS C 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (18960) covalent geometry : angle 0.61276 / 0.29 (25644) SS BOND : bond 0.00194 / 0.11 ( 12) SS BOND : angle 0.84582 / 0.49 ( 24) hydrogen bonds : bond 0.05384 / 3.54 ( 1182) hydrogen bonds : angle 3.06916 / 2.19 ( 3456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 213 time to evaluate : 0.757 Fit side-chains REVERT: A 122 MET cc_start: 0.8084 (mmt) cc_final: 0.7511 (mmt) REVERT: A 129 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.7976 (mtm-85) REVERT: A 190 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.6556 (m-70) REVERT: A 206 TYR cc_start: 0.6238 (m-10) cc_final: 0.5873 (m-10) REVERT: A 229 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7428 (t80) REVERT: A 258 ILE cc_start: 0.8072 (tt) cc_final: 0.7834 (tt) REVERT: A 261 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7157 (pp) REVERT: B 122 MET cc_start: 0.8041 (mmt) cc_final: 0.7737 (mmt) REVERT: B 155 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8086 (tt) REVERT: B 166 MET cc_start: 0.8337 (mmm) cc_final: 0.8004 (mmp) REVERT: B 204 ARG cc_start: 0.8160 (ttt180) cc_final: 0.7413 (tpt170) REVERT: B 258 ILE cc_start: 0.7971 (tt) cc_final: 0.7698 (tt) REVERT: B 261 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7696 (pp) REVERT: B 268 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7648 (pp) REVERT: C 122 MET cc_start: 0.7794 (mmt) cc_final: 0.7387 (mmt) REVERT: C 129 ARG cc_start: 0.8258 (mmm-85) cc_final: 0.7787 (mtm-85) REVERT: C 155 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7853 (tt) REVERT: C 204 ARG cc_start: 0.8117 (tpt170) cc_final: 0.7559 (ttt90) REVERT: C 258 ILE cc_start: 0.8211 (tt) cc_final: 0.7888 (tt) REVERT: D 122 MET cc_start: 0.8080 (mmt) cc_final: 0.7499 (mmt) REVERT: D 129 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.7958 (mtm-85) REVERT: D 190 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.6556 (m-70) REVERT: D 229 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7417 (t80) REVERT: E 122 MET cc_start: 0.8033 (mmt) cc_final: 0.7726 (mmt) REVERT: E 155 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8102 (tt) REVERT: E 206 TYR cc_start: 0.6138 (m-10) cc_final: 0.5850 (m-10) REVERT: E 258 ILE cc_start: 0.8056 (tt) cc_final: 0.7800 (tt) REVERT: E 261 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7508 (pp) REVERT: E 268 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7757 (pp) REVERT: F 122 MET cc_start: 0.8046 (mmt) cc_final: 0.7836 (mmt) REVERT: F 129 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.7742 (mtm-85) REVERT: F 155 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7868 (tt) REVERT: F 204 ARG cc_start: 0.8204 (tpt170) cc_final: 0.7760 (ttt90) REVERT: F 258 ILE cc_start: 0.8196 (tt) cc_final: 0.7863 (tt) REVERT: F 303 MET cc_start: 0.7269 (mpp) cc_final: 0.6976 (mtm) outliers start: 75 outliers final: 56 residues processed: 270 average time/residue: 0.1378 time to fit residues: 57.8453 Evaluate side-chains 280 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 211 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 229 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 419 TYR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 76 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 138 ASN B 322 HIS E 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.154100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.112529 restraints weight = 23727.463| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.76 r_work: 0.3348 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18972 Z= 0.137 Angle : 0.605 11.327 25668 Z= 0.284 Chirality : 0.040 0.164 3000 Planarity : 0.003 0.036 2904 Dihedral : 10.999 94.377 3078 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.85 % Allowed : 12.93 % Favored : 83.23 % 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: 2.37 (0.19), residues: 2142 helix: 2.81 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.51 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.010 0.001 TYR A 419 PHE 0.010 0.001 PHE D 177 TRP 0.008 0.001 TRP B 288 HIS 0.002 0.000 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (18960) covalent geometry : angle 0.60511 / 0.28 (25644) SS BOND : bond 0.00198 / 0.11 ( 12) SS BOND : angle 0.85513 / 0.48 ( 24) hydrogen bonds : bond 0.05222 / 3.43 ( 1182) hydrogen bonds : angle 3.05371 / 2.18 ( 3456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3367.47 seconds wall clock time: 58 minutes 59.32 seconds (3539.32 seconds total)