Starting phenix.real_space_refine on Wed Nov 19 02:08:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sp2_10279/11_2025/6sp2_10279.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sp2_10279/11_2025/6sp2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6sp2_10279/11_2025/6sp2_10279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sp2_10279/11_2025/6sp2_10279.map" model { file = "/net/cci-nas-00/data/ceres_data/6sp2_10279/11_2025/6sp2_10279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sp2_10279/11_2025/6sp2_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-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18498 Number of models: 1 Model: "" Number of chains: 7 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: "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: 72 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: 72 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: 72 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: 72 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: 72 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: 72 Unresolved non-hydrogen chiralities: 10 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 3.49, per 1000 atoms: 0.19 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 C 71 " - pdb=" SG CYS C 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS F 71 " - pdb=" SG CYS F 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 238 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 238 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS E 238 " - pdb=" SG CYS E 299 " distance=2.03 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: 1.80 Conformation dependent library (CDL) restraints added in 795.8 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: 0.54 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: 2.88 Time building geometry restraints manager: 2.33 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: 24831 2.20 - 4.41: 692 4.41 - 6.61: 102 6.61 - 8.81: 7 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 - 33.93: 11352 33.93 - 67.87: 450 67.87 - 101.80: 120 101.80 - 135.73: 84 135.73 - 169.67: 24 Dihedral angle restraints: 12030 sinusoidal: 5682 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 12027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2037 0.043 - 0.085: 741 0.085 - 0.128: 166 0.128 - 0.171: 44 0.171 - 0.213: 12 Chirality restraints: 3000 Sorted by residual: chirality pdb=" CA PRO F 69 " pdb=" N PRO F 69 " pdb=" C PRO F 69 " pdb=" CB PRO F 69 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA PRO A 69 " pdb=" N PRO A 69 " pdb=" C PRO A 69 " pdb=" CB PRO A 69 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA PRO B 69 " pdb=" N PRO B 69 " pdb=" C PRO B 69 " pdb=" CB PRO B 69 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.580 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 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 0.050 18972 Z= 0.290 Angle : 0.843 11.015 25668 Z= 0.429 Chirality : 0.048 0.213 3000 Planarity : 0.005 0.041 2904 Dihedral : 23.274 169.667 7914 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 covalent geometry : bond 0.00553 (18960) covalent geometry : angle 0.83991 (25644) SS BOND : bond 0.00690 ( 12) SS BOND : angle 2.51383 ( 24) hydrogen bonds : bond 0.12815 ( 1182) hydrogen bonds : angle 4.43918 ( 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 : 0.626 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: 0.6592 (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: 0.7052 (mtm) cc_final: 0.6456 (mtp) REVERT: B 122 MET cc_start: 0.7520 (mmt) cc_final: 0.6984 (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: 0.7216 (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: 0.1439 time to fit residues: 67.9661 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 : 0.666 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 136 GLN 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.155485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.114388 restraints weight = 23238.603| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.69 r_work: 0.3364 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18972 Z= 0.156 Angle : 0.715 12.142 25668 Z= 0.324 Chirality : 0.046 0.287 3000 Planarity : 0.004 0.034 2904 Dihedral : 24.132 162.076 4308 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.03 % Allowed : 8.33 % Favored : 89.64 % 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 : -1.70 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 106 TYR 0.011 0.001 TYR A 419 PHE 0.010 0.001 PHE A 177 TRP 0.015 0.002 TRP E 288 HIS 0.003 0.001 HIS C 422 Details of bonding type rmsd covalent geometry : bond 0.00351 (18960) covalent geometry : angle 0.71396 (25644) SS BOND : bond 0.00222 ( 12) SS BOND : angle 1.32797 ( 24) hydrogen bonds : bond 0.05744 ( 1182) hydrogen bonds : angle 3.39278 ( 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 253 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.669 Fit side-chains REVERT: A 122 MET cc_start: 0.8112 (mmt) cc_final: 0.7495 (mmt) REVERT: A 166 MET cc_start: 0.8050 (mmm) cc_final: 0.7642 (mmt) REVERT: A 271 SER cc_start: 0.8839 (t) cc_final: 0.8537 (t) REVERT: A 413 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7584 (mpp) REVERT: A 435 MET cc_start: 0.7772 (ptm) cc_final: 0.7571 (ptt) REVERT: B 102 MET cc_start: 0.8119 (mtm) cc_final: 0.7732 (mtp) REVERT: B 122 MET cc_start: 0.8301 (mmt) cc_final: 0.7704 (mmt) REVERT: B 303 MET cc_start: 0.6202 (mmm) cc_final: 0.5280 (mmt) REVERT: C 122 MET cc_start: 0.7869 (mmt) cc_final: 0.7527 (mmt) REVERT: C 129 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7820 (mtm-85) REVERT: C 204 ARG cc_start: 0.8200 (tpt170) cc_final: 0.7383 (ttt180) REVERT: D 122 MET cc_start: 0.8064 (mmt) cc_final: 0.7460 (mmt) REVERT: D 166 MET cc_start: 0.8072 (mmm) cc_final: 0.7657 (mmt) REVERT: D 271 SER cc_start: 0.8826 (t) cc_final: 0.8522 (t) REVERT: D 413 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.7600 (mpp) REVERT: D 435 MET cc_start: 0.7807 (ptm) cc_final: 0.7604 (ptt) REVERT: E 102 MET cc_start: 0.8124 (mtm) cc_final: 0.7716 (mtp) REVERT: E 122 MET cc_start: 0.8237 (mmt) cc_final: 0.7652 (mmt) REVERT: E 303 MET cc_start: 0.6198 (mmm) cc_final: 0.5321 (mmt) REVERT: F 122 MET cc_start: 0.7913 (mmt) cc_final: 0.7431 (mmt) REVERT: F 129 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7881 (mtm-85) REVERT: F 204 ARG cc_start: 0.8129 (tpt170) cc_final: 0.7375 (ttt180) REVERT: F 297 LYS cc_start: 0.9045 (ptmm) cc_final: 0.8841 (tttp) outliers start: 38 outliers final: 34 residues processed: 237 average time/residue: 0.1499 time to fit residues: 53.8037 Evaluate side-chains 234 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 D residue 413 MET 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 145 LEU 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: 0.7980 chunk 214 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 165 optimal weight: 0.3980 chunk 143 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN C 136 GLN E 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.156635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114940 restraints weight = 23399.510| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.72 r_work: 0.3377 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18972 Z= 0.133 Angle : 0.638 11.492 25668 Z= 0.292 Chirality : 0.044 0.285 3000 Planarity : 0.003 0.030 2904 Dihedral : 20.967 163.237 4308 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.67 % Allowed : 11.06 % Favored : 86.27 % 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: 1.73 (0.19), residues: 2142 helix: 2.22 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.48 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 39 TYR 0.009 0.001 TYR D 419 PHE 0.009 0.001 PHE F 404 TRP 0.011 0.001 TRP B 288 HIS 0.002 0.001 HIS C 401 Details of bonding type rmsd covalent geometry : bond 0.00296 (18960) covalent geometry : angle 0.63747 (25644) SS BOND : bond 0.00076 ( 12) SS BOND : angle 0.72514 ( 24) hydrogen bonds : bond 0.05112 ( 1182) hydrogen bonds : angle 3.16394 ( 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 262 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 212 time to evaluate : 0.693 Fit side-chains REVERT: A 122 MET cc_start: 0.7902 (mmt) cc_final: 0.7531 (tpp) REVERT: A 166 MET cc_start: 0.8045 (mmm) cc_final: 0.7655 (mmt) REVERT: A 271 SER cc_start: 0.8814 (t) cc_final: 0.8498 (t) REVERT: B 102 MET cc_start: 0.8025 (mtm) cc_final: 0.7656 (mtp) REVERT: B 122 MET cc_start: 0.7932 (mmt) cc_final: 0.7346 (mmt) REVERT: B 166 MET cc_start: 0.7937 (mmm) cc_final: 0.7673 (mmp) REVERT: B 397 TRP cc_start: 0.8303 (m-10) cc_final: 0.8101 (m-10) REVERT: C 122 MET cc_start: 0.7810 (mmt) cc_final: 0.7331 (mmt) REVERT: C 129 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.7820 (mtm-85) REVERT: C 204 ARG cc_start: 0.8310 (tpt170) cc_final: 0.7515 (ttt180) REVERT: C 303 MET cc_start: 0.7331 (mpp) cc_final: 0.6732 (mtm) REVERT: D 122 MET cc_start: 0.7901 (mmt) cc_final: 0.7516 (tpp) REVERT: D 166 MET cc_start: 0.8063 (mmm) cc_final: 0.7662 (mmt) REVERT: D 271 SER cc_start: 0.8806 (t) cc_final: 0.8515 (t) REVERT: E 102 MET cc_start: 0.8042 (mtm) cc_final: 0.7671 (mtp) REVERT: E 122 MET cc_start: 0.7918 (mmt) cc_final: 0.7339 (mmt) REVERT: E 397 TRP cc_start: 0.8296 (m-10) cc_final: 0.8087 (m-10) REVERT: F 122 MET cc_start: 0.7761 (mmt) cc_final: 0.7245 (mmt) REVERT: F 129 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.7795 (mtm-85) REVERT: F 204 ARG cc_start: 0.8180 (tpt170) cc_final: 0.7427 (ttt180) REVERT: F 261 LEU cc_start: 0.7883 (pp) cc_final: 0.7615 (pp) REVERT: F 303 MET cc_start: 0.7556 (mpp) cc_final: 0.6752 (mtm) outliers start: 50 outliers final: 40 residues processed: 238 average time/residue: 0.1452 time to fit residues: 53.2019 Evaluate side-chains 243 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 226 THR 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 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 146 ILE Chi-restraints excluded: chain C residue 226 THR 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 226 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 411 VAL 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 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 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: 0.9980 chunk 46 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 76 optimal weight: 0.0020 chunk 178 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 201 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN E 136 GLN F 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.157388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115323 restraints weight = 23376.541| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.75 r_work: 0.3379 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2592 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= 0.126 Angle : 0.604 11.363 25668 Z= 0.283 Chirality : 0.042 0.185 3000 Planarity : 0.003 0.065 2904 Dihedral : 19.553 161.503 4308 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.26 % Allowed : 11.06 % 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: 1.99 (0.19), residues: 2142 helix: 2.44 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 39 TYR 0.009 0.001 TYR F 97 PHE 0.009 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 covalent geometry : bond 0.00278 (18960) covalent geometry : angle 0.60274 (25644) SS BOND : bond 0.00123 ( 12) SS BOND : angle 1.20934 ( 24) hydrogen bonds : bond 0.04926 ( 1182) hydrogen bonds : angle 3.09995 ( 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 270 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 0.714 Fit side-chains REVERT: A 122 MET cc_start: 0.7796 (mmt) cc_final: 0.7451 (tpp) REVERT: A 166 MET cc_start: 0.8230 (mmm) cc_final: 0.7755 (mmt) REVERT: A 271 SER cc_start: 0.8862 (t) cc_final: 0.8574 (t) REVERT: B 122 MET cc_start: 0.7817 (mmt) cc_final: 0.7307 (mmt) REVERT: B 166 MET cc_start: 0.8001 (mmm) cc_final: 0.7692 (mmp) REVERT: B 397 TRP cc_start: 0.8230 (m-10) cc_final: 0.8014 (m-10) REVERT: C 122 MET cc_start: 0.7708 (mmt) cc_final: 0.7191 (mmt) REVERT: C 129 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7805 (mtm-85) REVERT: C 204 ARG cc_start: 0.8289 (tpt170) cc_final: 0.7451 (ttt180) REVERT: C 303 MET cc_start: 0.7301 (mpp) cc_final: 0.6677 (mtm) REVERT: D 122 MET cc_start: 0.7792 (mmt) cc_final: 0.7429 (tpp) REVERT: D 166 MET cc_start: 0.8241 (mmm) cc_final: 0.7752 (mmt) REVERT: D 271 SER cc_start: 0.8835 (t) cc_final: 0.8539 (t) REVERT: E 122 MET cc_start: 0.7803 (mmt) cc_final: 0.7295 (mmt) REVERT: E 258 ILE cc_start: 0.7865 (tt) cc_final: 0.7587 (tt) REVERT: E 397 TRP cc_start: 0.8198 (m-10) cc_final: 0.7970 (m-10) REVERT: F 122 MET cc_start: 0.7671 (mmt) cc_final: 0.7153 (mmt) REVERT: F 129 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.7813 (mtm-85) REVERT: F 204 ARG cc_start: 0.8197 (tpt170) cc_final: 0.7440 (ttt180) REVERT: F 303 MET cc_start: 0.7588 (mpp) cc_final: 0.6829 (mtm) outliers start: 61 outliers final: 43 residues processed: 251 average time/residue: 0.1400 time to fit residues: 54.3190 Evaluate side-chains 244 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 55 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 146 ILE Chi-restraints excluded: chain E residue 226 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 58 optimal weight: 0.0970 chunk 140 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.152251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111083 restraints weight = 23623.856| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.72 r_work: 0.3328 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18972 Z= 0.155 Angle : 0.637 11.851 25668 Z= 0.301 Chirality : 0.042 0.163 3000 Planarity : 0.004 0.065 2904 Dihedral : 18.897 159.333 4308 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.43 % Allowed : 10.04 % Favored : 85.52 % 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: 1.98 (0.19), residues: 2142 helix: 2.45 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.47 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 39 TYR 0.014 0.001 TYR A 419 PHE 0.010 0.001 PHE D 177 TRP 0.012 0.001 TRP B 288 HIS 0.002 0.000 HIS C 401 Details of bonding type rmsd covalent geometry : bond 0.00362 (18960) covalent geometry : angle 0.63505 (25644) SS BOND : bond 0.00237 ( 12) SS BOND : angle 1.61693 ( 24) hydrogen bonds : bond 0.05866 ( 1182) hydrogen bonds : angle 3.24159 ( 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 289 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 206 time to evaluate : 0.702 Fit side-chains REVERT: A 122 MET cc_start: 0.8204 (mmt) cc_final: 0.7660 (mmt) REVERT: A 166 MET cc_start: 0.8466 (mmm) cc_final: 0.7869 (mmt) REVERT: A 229 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7168 (t80) REVERT: A 261 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7265 (pp) REVERT: A 271 SER cc_start: 0.8870 (t) cc_final: 0.8563 (t) REVERT: B 122 MET cc_start: 0.8316 (mmt) cc_final: 0.7830 (mmt) REVERT: B 166 MET cc_start: 0.8265 (mmm) cc_final: 0.7901 (mmp) REVERT: B 268 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7674 (pp) REVERT: C 122 MET cc_start: 0.8012 (mmt) cc_final: 0.7769 (mmt) REVERT: C 129 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.7773 (mtm-85) REVERT: C 155 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8035 (tt) REVERT: C 204 ARG cc_start: 0.8274 (tpt170) cc_final: 0.7450 (ttt180) REVERT: C 303 MET cc_start: 0.7525 (mpp) cc_final: 0.6918 (mtm) REVERT: D 122 MET cc_start: 0.8195 (mmt) cc_final: 0.7639 (mmt) REVERT: D 129 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.7948 (mtm-85) REVERT: D 166 MET cc_start: 0.8494 (mmm) cc_final: 0.7905 (mmt) REVERT: D 190 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.6482 (m-70) REVERT: D 229 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7157 (t80) REVERT: D 271 SER cc_start: 0.8913 (t) cc_final: 0.8575 (t) REVERT: E 122 MET cc_start: 0.8323 (mmt) cc_final: 0.7849 (mmt) REVERT: E 258 ILE cc_start: 0.7970 (tt) cc_final: 0.7671 (tt) REVERT: E 261 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7744 (pp) REVERT: E 268 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7778 (pp) REVERT: F 122 MET cc_start: 0.7999 (mmt) cc_final: 0.7771 (mmt) REVERT: F 129 ARG cc_start: 0.8298 (mmm-85) cc_final: 0.7768 (mtm-85) REVERT: F 155 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8034 (tt) REVERT: F 204 ARG cc_start: 0.8237 (tpt170) cc_final: 0.7429 (ttt180) REVERT: F 303 MET cc_start: 0.7581 (mpp) cc_final: 0.6963 (mtm) outliers start: 83 outliers final: 67 residues processed: 267 average time/residue: 0.1529 time to fit residues: 62.1094 Evaluate side-chains 281 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 205 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 72 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 229 TYR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 VAL 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 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 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 264 VAL 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 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 273 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 352 VAL 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 72 ILE 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 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 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 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 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 264 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 25 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 206 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN D 136 GLN E 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.155391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113750 restraints weight = 23372.311| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.74 r_work: 0.3361 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2941 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 : 0.592 11.199 25668 Z= 0.278 Chirality : 0.041 0.158 3000 Planarity : 0.003 0.052 2904 Dihedral : 18.097 158.458 4308 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.27 % Allowed : 10.74 % 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: 2.39 (0.19), residues: 2142 helix: 2.82 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.24 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.009 0.001 TYR A 419 PHE 0.009 0.001 PHE D 177 TRP 0.007 0.001 TRP B 288 HIS 0.002 0.000 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00289 (18960) covalent geometry : angle 0.59132 (25644) SS BOND : bond 0.00201 ( 12) SS BOND : angle 1.15617 ( 24) hydrogen bonds : bond 0.05065 ( 1182) hydrogen bonds : angle 3.09150 ( 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 292 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 212 time to evaluate : 0.685 Fit side-chains REVERT: A 122 MET cc_start: 0.7845 (mmt) cc_final: 0.7476 (tpp) REVERT: A 129 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.7930 (mtm-85) REVERT: A 166 MET cc_start: 0.8308 (mmm) cc_final: 0.7933 (tpp) REVERT: A 190 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.6565 (m-70) REVERT: A 229 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7263 (t80) REVERT: A 258 ILE cc_start: 0.8034 (tt) cc_final: 0.7814 (tt) REVERT: A 261 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7129 (pp) REVERT: A 304 PHE cc_start: 0.7730 (m-10) cc_final: 0.7367 (m-10) REVERT: B 122 MET cc_start: 0.7906 (mmt) cc_final: 0.7395 (mmt) REVERT: B 166 MET cc_start: 0.8126 (mmm) cc_final: 0.7781 (mmp) REVERT: B 258 ILE cc_start: 0.7980 (tt) cc_final: 0.7660 (tt) REVERT: C 122 MET cc_start: 0.7771 (mmt) cc_final: 0.7280 (mmt) REVERT: C 129 ARG cc_start: 0.8240 (mmm-85) cc_final: 0.7746 (mtm-85) REVERT: C 204 ARG cc_start: 0.8278 (tpt170) cc_final: 0.7440 (ttt180) REVERT: C 303 MET cc_start: 0.7497 (mpp) cc_final: 0.6938 (mtm) REVERT: D 122 MET cc_start: 0.7863 (mmt) cc_final: 0.7481 (tpp) REVERT: D 129 ARG cc_start: 0.8360 (mmm-85) cc_final: 0.7936 (mtm-85) REVERT: D 166 MET cc_start: 0.8319 (mmm) cc_final: 0.7936 (tpp) REVERT: D 190 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.6556 (m-70) REVERT: D 229 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7331 (t80) REVERT: D 271 SER cc_start: 0.8911 (t) cc_final: 0.8580 (t) REVERT: D 304 PHE cc_start: 0.7752 (m-10) cc_final: 0.7382 (m-10) REVERT: E 122 MET cc_start: 0.7897 (mmt) cc_final: 0.7381 (mmt) REVERT: E 258 ILE cc_start: 0.7948 (tt) cc_final: 0.7646 (tt) REVERT: E 261 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7691 (pp) REVERT: E 268 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7669 (pp) REVERT: F 122 MET cc_start: 0.7740 (mmt) cc_final: 0.7269 (mmt) REVERT: F 129 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.7773 (mtm-85) REVERT: F 204 ARG cc_start: 0.8306 (tpt170) cc_final: 0.7808 (ttt90) REVERT: F 303 MET cc_start: 0.7432 (mpp) cc_final: 0.6889 (mtm) outliers start: 80 outliers final: 60 residues processed: 270 average time/residue: 0.1469 time to fit residues: 60.7083 Evaluate side-chains 273 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 206 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR 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 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 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 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 130 ASP 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 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 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: 0.8980 chunk 72 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 195 optimal weight: 0.2980 chunk 145 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.153772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.112508 restraints weight = 23685.618| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.73 r_work: 0.3344 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18972 Z= 0.136 Angle : 0.605 11.443 25668 Z= 0.284 Chirality : 0.041 0.164 3000 Planarity : 0.003 0.047 2904 Dihedral : 17.638 156.067 4308 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.49 % Allowed : 11.38 % 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: 2.44 (0.19), residues: 2142 helix: 2.87 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.011 0.001 TYR A 419 PHE 0.010 0.001 PHE D 177 TRP 0.008 0.001 TRP E 288 HIS 0.003 0.000 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00310 (18960) covalent geometry : angle 0.60461 (25644) SS BOND : bond 0.00178 ( 12) SS BOND : angle 1.12624 ( 24) hydrogen bonds : bond 0.05300 ( 1182) hydrogen bonds : angle 3.10960 ( 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 294 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 210 time to evaluate : 0.621 Fit side-chains REVERT: A 122 MET cc_start: 0.8031 (mmt) cc_final: 0.7447 (mmt) REVERT: A 129 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.7933 (mtm-85) REVERT: A 190 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.6508 (m-70) REVERT: A 229 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.7362 (t80) REVERT: A 258 ILE cc_start: 0.8045 (tt) cc_final: 0.7813 (tt) REVERT: A 261 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7145 (pp) REVERT: B 122 MET cc_start: 0.8024 (mmt) cc_final: 0.7529 (mmt) REVERT: B 166 MET cc_start: 0.8174 (mmm) cc_final: 0.7811 (mmp) REVERT: B 258 ILE cc_start: 0.8030 (tt) cc_final: 0.7770 (tt) REVERT: B 268 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7611 (pp) REVERT: C 122 MET cc_start: 0.7867 (mmt) cc_final: 0.7437 (mmt) REVERT: C 129 ARG cc_start: 0.8251 (mmm-85) cc_final: 0.7758 (mtm-85) REVERT: C 155 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7954 (tt) REVERT: C 204 ARG cc_start: 0.8170 (tpt170) cc_final: 0.7203 (ttt180) REVERT: C 303 MET cc_start: 0.7543 (mpp) cc_final: 0.6995 (mtm) REVERT: D 122 MET cc_start: 0.8012 (mmt) cc_final: 0.7427 (mmt) REVERT: D 129 ARG cc_start: 0.8351 (mmm-85) cc_final: 0.7938 (mtm-85) REVERT: D 190 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.6511 (m-70) REVERT: D 206 TYR cc_start: 0.6029 (m-10) cc_final: 0.5669 (m-10) REVERT: D 229 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7357 (t80) REVERT: E 122 MET cc_start: 0.8101 (mmt) cc_final: 0.7648 (mmt) REVERT: E 206 TYR cc_start: 0.5924 (m-10) cc_final: 0.5586 (m-10) REVERT: E 258 ILE cc_start: 0.8059 (tt) cc_final: 0.7820 (tt) REVERT: E 261 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7709 (pp) REVERT: E 268 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7691 (pp) REVERT: F 122 MET cc_start: 0.7850 (mmt) cc_final: 0.7403 (mmt) REVERT: F 129 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7742 (mtm-85) REVERT: F 155 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7969 (tt) REVERT: F 204 ARG cc_start: 0.8325 (tpt170) cc_final: 0.7886 (ttt90) REVERT: F 303 MET cc_start: 0.7503 (mpp) cc_final: 0.6989 (mtm) REVERT: F 419 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.6833 (p90) outliers start: 84 outliers final: 65 residues processed: 268 average time/residue: 0.1421 time to fit residues: 58.4011 Evaluate side-chains 283 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 207 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 268 LEU 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 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 145 LEU 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 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 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 264 VAL 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 145 LEU 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 Chi-restraints excluded: chain F residue 419 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 200 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 165 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.154442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113131 restraints weight = 23364.781| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.73 r_work: 0.3354 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3162 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= 0.131 Angle : 0.601 11.271 25668 Z= 0.282 Chirality : 0.041 0.168 3000 Planarity : 0.003 0.043 2904 Dihedral : 17.249 153.312 4308 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.43 % Allowed : 11.75 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.19), residues: 2142 helix: 2.92 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.24 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.009 0.001 TYR A 419 PHE 0.009 0.001 PHE D 177 TRP 0.007 0.001 TRP B 288 HIS 0.002 0.000 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00299 (18960) covalent geometry : angle 0.60010 (25644) SS BOND : bond 0.00179 ( 12) SS BOND : angle 1.00850 ( 24) hydrogen bonds : bond 0.05099 ( 1182) hydrogen bonds : angle 3.06398 ( 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 291 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 208 time to evaluate : 0.688 Fit side-chains REVERT: A 122 MET cc_start: 0.7877 (mmt) cc_final: 0.7520 (tpp) REVERT: A 129 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.7954 (mtm-85) REVERT: A 190 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.6600 (m-70) REVERT: A 206 TYR cc_start: 0.6138 (m-10) cc_final: 0.5873 (m-10) REVERT: A 229 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7368 (t80) REVERT: A 258 ILE cc_start: 0.8052 (tt) cc_final: 0.7820 (tt) REVERT: A 261 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7095 (pp) REVERT: A 413 MET cc_start: 0.8637 (tpp) cc_final: 0.8400 (mmm) REVERT: B 122 MET cc_start: 0.7935 (mmt) cc_final: 0.7425 (mmt) REVERT: B 166 MET cc_start: 0.8136 (mmm) cc_final: 0.7791 (mmp) REVERT: B 206 TYR cc_start: 0.5885 (m-10) cc_final: 0.5555 (m-10) REVERT: B 258 ILE cc_start: 0.8015 (tt) cc_final: 0.7746 (tt) REVERT: B 268 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7528 (pp) REVERT: C 122 MET cc_start: 0.7766 (mmt) cc_final: 0.7309 (mmt) REVERT: C 129 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.7808 (mtm-85) REVERT: C 155 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7874 (tt) REVERT: C 204 ARG cc_start: 0.8157 (tpt170) cc_final: 0.7593 (ttt90) REVERT: C 303 MET cc_start: 0.7477 (mpp) cc_final: 0.6988 (mtm) REVERT: D 122 MET cc_start: 0.7867 (mmt) cc_final: 0.7505 (tpp) REVERT: D 129 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.7944 (mtm-85) REVERT: D 190 HIS cc_start: 0.7936 (OUTLIER) cc_final: 0.6611 (m-70) REVERT: D 206 TYR cc_start: 0.6090 (m-10) cc_final: 0.5767 (m-10) REVERT: D 229 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.7363 (t80) REVERT: D 413 MET cc_start: 0.8651 (tpp) cc_final: 0.8416 (mmm) REVERT: E 122 MET cc_start: 0.7927 (mmt) cc_final: 0.7434 (mmt) REVERT: E 206 TYR cc_start: 0.5947 (m-10) cc_final: 0.5653 (m-10) REVERT: E 258 ILE cc_start: 0.8034 (tt) cc_final: 0.7788 (tt) REVERT: E 261 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7645 (pp) REVERT: E 268 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7566 (pp) REVERT: F 122 MET cc_start: 0.7744 (mmt) cc_final: 0.7273 (mmt) REVERT: F 129 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.7765 (mtm-85) REVERT: F 155 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7895 (tt) REVERT: F 204 ARG cc_start: 0.8237 (tpt170) cc_final: 0.7792 (ttt90) REVERT: F 303 MET cc_start: 0.7543 (mpp) cc_final: 0.7144 (mtm) REVERT: F 419 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.6838 (p90) outliers start: 83 outliers final: 63 residues processed: 269 average time/residue: 0.1437 time to fit residues: 58.9353 Evaluate side-chains 279 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 205 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 264 VAL 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 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 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR 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 145 LEU 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 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 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 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 264 VAL 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 145 LEU 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 Chi-restraints excluded: chain F residue 419 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 8 optimal weight: 0.0030 chunk 82 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 199 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 203 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 ASN F 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.157145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115610 restraints weight = 23422.468| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.74 r_work: 0.3385 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3279 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= 0.117 Angle : 0.583 11.102 25668 Z= 0.272 Chirality : 0.040 0.166 3000 Planarity : 0.003 0.042 2904 Dihedral : 16.835 150.506 4308 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.79 % Allowed : 12.66 % Favored : 83.55 % 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: 3.03 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.28 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.007 0.001 TYR D 419 PHE 0.009 0.001 PHE D 177 TRP 0.006 0.001 TRP D 418 HIS 0.003 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00259 (18960) covalent geometry : angle 0.58270 (25644) SS BOND : bond 0.00185 ( 12) SS BOND : angle 0.92425 ( 24) hydrogen bonds : bond 0.04634 ( 1182) hydrogen bonds : angle 2.96678 ( 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 295 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 224 time to evaluate : 0.719 Fit side-chains REVERT: A 122 MET cc_start: 0.7798 (mmt) cc_final: 0.7462 (tpp) REVERT: A 129 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.7948 (mtm-85) REVERT: A 190 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.6605 (m-70) REVERT: A 206 TYR cc_start: 0.6048 (m-10) cc_final: 0.5818 (m-10) REVERT: A 229 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7400 (t80) REVERT: A 258 ILE cc_start: 0.8067 (tt) cc_final: 0.7836 (tt) REVERT: A 261 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.7047 (pp) REVERT: A 451 TRP cc_start: 0.7266 (t-100) cc_final: 0.6559 (t60) REVERT: B 122 MET cc_start: 0.7718 (mmt) cc_final: 0.7458 (mmt) REVERT: B 166 MET cc_start: 0.8038 (mmm) cc_final: 0.7685 (mmp) REVERT: B 206 TYR cc_start: 0.5874 (m-10) cc_final: 0.5575 (m-10) REVERT: B 258 ILE cc_start: 0.7972 (tt) cc_final: 0.7641 (tt) REVERT: B 268 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7509 (pp) REVERT: C 122 MET cc_start: 0.7466 (mmt) cc_final: 0.6964 (mmt) REVERT: C 129 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7799 (mtm-85) REVERT: C 155 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7830 (tt) REVERT: C 204 ARG cc_start: 0.8100 (tpt170) cc_final: 0.7526 (ttt90) REVERT: C 303 MET cc_start: 0.7195 (mpp) cc_final: 0.6936 (mtm) REVERT: D 122 MET cc_start: 0.7788 (mmt) cc_final: 0.7444 (tpp) REVERT: D 129 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7957 (mtm-85) REVERT: D 190 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.6605 (m-70) REVERT: D 206 TYR cc_start: 0.6183 (m-10) cc_final: 0.5867 (m-10) REVERT: D 229 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7396 (t80) REVERT: E 122 MET cc_start: 0.7723 (mmt) cc_final: 0.7168 (mmt) REVERT: E 206 TYR cc_start: 0.5947 (m-10) cc_final: 0.5673 (m-10) REVERT: E 258 ILE cc_start: 0.8028 (tt) cc_final: 0.7712 (tt) REVERT: E 261 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7612 (pp) REVERT: E 268 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7608 (pp) REVERT: F 102 MET cc_start: 0.8114 (mtm) cc_final: 0.7913 (mtp) REVERT: F 122 MET cc_start: 0.7445 (mmt) cc_final: 0.6960 (mmt) REVERT: F 129 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7811 (mtm-85) REVERT: F 155 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7851 (tt) REVERT: F 204 ARG cc_start: 0.8202 (tpt170) cc_final: 0.7761 (ttt90) REVERT: F 303 MET cc_start: 0.7513 (mpp) cc_final: 0.7208 (mtm) outliers start: 71 outliers final: 58 residues processed: 273 average time/residue: 0.1396 time to fit residues: 58.2580 Evaluate side-chains 285 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 217 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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 50 THR Chi-restraints excluded: chain B residue 55 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 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 145 LEU 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 55 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 E residue 50 THR Chi-restraints excluded: chain E residue 55 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 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 145 LEU 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: 6.9990 chunk 183 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 184 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.154774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.113155 restraints weight = 23493.718| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.76 r_work: 0.3368 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18972 Z= 0.135 Angle : 0.607 11.405 25668 Z= 0.286 Chirality : 0.040 0.159 3000 Planarity : 0.003 0.040 2904 Dihedral : 16.674 147.247 4308 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.74 % Allowed : 13.14 % Favored : 83.12 % 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: 2.55 (0.19), residues: 2142 helix: 2.98 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.28 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.011 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 E 134 Details of bonding type rmsd covalent geometry : bond 0.00309 (18960) covalent geometry : angle 0.60701 (25644) SS BOND : bond 0.00159 ( 12) SS BOND : angle 0.94122 ( 24) hydrogen bonds : bond 0.05194 ( 1182) hydrogen bonds : angle 3.04932 ( 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 284 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 214 time to evaluate : 0.696 Fit side-chains REVERT: A 122 MET cc_start: 0.8004 (mmt) cc_final: 0.7421 (mmt) REVERT: A 129 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7967 (mtm-85) REVERT: A 190 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.6608 (m-70) REVERT: A 206 TYR cc_start: 0.6178 (m-10) cc_final: 0.5951 (m-10) REVERT: A 229 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7408 (t80) REVERT: A 258 ILE cc_start: 0.8106 (tt) cc_final: 0.7868 (tt) REVERT: A 261 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7188 (pp) REVERT: A 451 TRP cc_start: 0.7386 (t-100) cc_final: 0.6689 (t60) REVERT: B 122 MET cc_start: 0.7973 (mmt) cc_final: 0.7693 (mmt) REVERT: B 166 MET cc_start: 0.8280 (mmm) cc_final: 0.7929 (mmp) REVERT: B 206 TYR cc_start: 0.6016 (m-10) cc_final: 0.5722 (m-10) REVERT: B 258 ILE cc_start: 0.8048 (tt) cc_final: 0.7771 (tt) REVERT: B 268 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7472 (pp) REVERT: C 129 ARG cc_start: 0.8251 (mmm-85) cc_final: 0.7821 (mtm-85) REVERT: C 155 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7913 (tt) REVERT: C 204 ARG cc_start: 0.8132 (tpt170) cc_final: 0.7576 (ttt90) REVERT: C 258 ILE cc_start: 0.8262 (tt) cc_final: 0.7930 (tt) REVERT: C 303 MET cc_start: 0.7320 (mpp) cc_final: 0.7112 (mtm) REVERT: D 122 MET cc_start: 0.8006 (mmt) cc_final: 0.7423 (mmt) REVERT: D 129 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.8037 (mtm-85) REVERT: D 190 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.6603 (m-70) REVERT: D 206 TYR cc_start: 0.6262 (m-10) cc_final: 0.5919 (m-10) REVERT: D 229 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7405 (t80) REVERT: E 122 MET cc_start: 0.8047 (mmt) cc_final: 0.7732 (mmt) REVERT: E 206 TYR cc_start: 0.6177 (m-10) cc_final: 0.5918 (m-10) REVERT: E 258 ILE cc_start: 0.8068 (tt) cc_final: 0.7785 (tt) REVERT: E 261 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7707 (pp) REVERT: E 268 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7687 (pp) REVERT: F 122 MET cc_start: 0.7844 (mmt) cc_final: 0.7394 (mmt) REVERT: F 129 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7827 (mtm-85) REVERT: F 155 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7931 (tt) REVERT: F 204 ARG cc_start: 0.8206 (tpt170) cc_final: 0.7781 (ttt90) REVERT: F 303 MET cc_start: 0.7382 (mpp) cc_final: 0.7142 (mtm) outliers start: 70 outliers final: 58 residues processed: 265 average time/residue: 0.1413 time to fit residues: 57.6242 Evaluate side-chains 279 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 211 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 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 50 THR Chi-restraints excluded: chain B residue 55 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 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 145 LEU 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 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 E residue 50 THR Chi-restraints excluded: chain E residue 55 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 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 145 LEU 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: 0.0040 chunk 130 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN B 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.156193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.114639 restraints weight = 23493.898| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.74 r_work: 0.3390 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3376 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= 0.123 Angle : 0.595 11.110 25668 Z= 0.280 Chirality : 0.040 0.162 3000 Planarity : 0.003 0.041 2904 Dihedral : 16.468 147.848 4308 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.58 % Allowed : 13.30 % Favored : 83.12 % 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: 2.62 (0.19), residues: 2142 helix: 3.05 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.29 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.012 0.001 TYR D 97 PHE 0.009 0.001 PHE A 177 TRP 0.006 0.001 TRP C 140 HIS 0.002 0.000 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00277 (18960) covalent geometry : angle 0.59427 (25644) SS BOND : bond 0.00216 ( 12) SS BOND : angle 1.29002 ( 24) hydrogen bonds : bond 0.04856 ( 1182) hydrogen bonds : angle 3.00745 ( 3456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3667.78 seconds wall clock time: 64 minutes 1.43 seconds (3841.43 seconds total)