Starting phenix.real_space_refine on Thu Mar 5 05:41:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sp2_10279/03_2026/6sp2_10279.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sp2_10279/03_2026/6sp2_10279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sp2_10279/03_2026/6sp2_10279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sp2_10279/03_2026/6sp2_10279.map" model { file = "/net/cci-nas-00/data/ceres_data/6sp2_10279/03_2026/6sp2_10279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sp2_10279/03_2026/6sp2_10279.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.136 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 156 5.16 5 C 12336 2.51 5 N 2640 2.21 5 O 3348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18498 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "B" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "C" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "D" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "E" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "F" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "A" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 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 Time building chain proxies: 4.77, per 1000 atoms: 0.26 Number of scatterers: 18498 At special positions: 0 Unit cell: (133.86, 144.9, 78.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 P 18 15.00 O 3348 8.00 N 2640 7.00 C 12336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 238 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS B 238 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 95 " distance=2.04 Simple disulfide: pdb=" SG CYS C 238 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 238 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 238 " - pdb=" SG CYS E 299 " distance=2.03 Simple disulfide: pdb=" SG CYS F 71 " - pdb=" SG CYS F 95 " distance=2.04 Simple disulfide: pdb=" SG CYS F 238 " - pdb=" SG CYS F 299 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 758.7 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: 0.44 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: 2.74 Time building geometry restraints manager: 2.32 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 17.730 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.810 ------------------------------------------------------------------------------- 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 : 0.544 Fit side-chains REVERT: A 122 MET cc_start: 0.7416 (mmt) cc_final: 0.6781 (mmt) REVERT: A 166 MET cc_start: 0.7177 (mmm) cc_final: 0.6593 (mmt) REVERT: A 204 ARG cc_start: 0.7555 (mtp180) cc_final: 0.7216 (ttt-90) REVERT: A 271 SER cc_start: 0.8203 (t) cc_final: 0.7910 (t) REVERT: B 102 MET cc_start: 0.7053 (mtm) cc_final: 0.6456 (mtp) REVERT: B 122 MET cc_start: 0.7520 (mmt) cc_final: 0.6983 (mmt) REVERT: B 297 LYS cc_start: 0.9076 (ptmm) cc_final: 0.8721 (tttp) REVERT: B 298 GLU cc_start: 0.8257 (tp30) cc_final: 0.7959 (tp30) REVERT: C 102 MET cc_start: 0.6711 (mtm) cc_final: 0.6242 (mtp) REVERT: C 122 MET cc_start: 0.7250 (mmt) cc_final: 0.6942 (mmt) REVERT: C 271 SER cc_start: 0.8511 (t) cc_final: 0.8282 (t) REVERT: C 297 LYS cc_start: 0.8978 (ptmm) cc_final: 0.8644 (tttp) REVERT: C 298 GLU cc_start: 0.8265 (tp30) cc_final: 0.8056 (tp30) REVERT: D 122 MET cc_start: 0.7347 (mmt) cc_final: 0.6704 (mmt) REVERT: D 166 MET cc_start: 0.7217 (mmm) cc_final: 0.6623 (mmt) REVERT: D 204 ARG cc_start: 0.7674 (mtp180) cc_final: 0.7388 (ttt-90) REVERT: D 271 SER cc_start: 0.8245 (t) cc_final: 0.7947 (t) REVERT: E 102 MET cc_start: 0.7027 (mtm) cc_final: 0.6372 (mtp) REVERT: E 122 MET cc_start: 0.7538 (mmt) cc_final: 0.7021 (mmt) REVERT: E 297 LYS cc_start: 0.9089 (ptmm) cc_final: 0.8697 (tttp) REVERT: F 122 MET cc_start: 0.7240 (mmt) cc_final: 0.6956 (mmt) REVERT: F 271 SER cc_start: 0.8010 (t) cc_final: 0.7740 (t) REVERT: F 297 LYS cc_start: 0.8989 (ptmm) cc_final: 0.8640 (tttp) REVERT: F 298 GLU cc_start: 0.8287 (tp30) cc_final: 0.8077 (tp30) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.1363 time to fit residues: 64.9038 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 : 0.631 ------------------------------------------------------------------------------- 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 : 0.492 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: 0.1371 time to fit residues: 49.3990 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 : 0.520 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.114944 restraints weight = 23399.523| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.72 r_work: 0.3380 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 0.72523 ( 24) hydrogen bonds : bond 0.05112 ( 1182) hydrogen bonds : angle 3.16393 ( 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 : 0.645 Fit side-chains REVERT: A 122 MET cc_start: 0.7904 (mmt) cc_final: 0.7532 (tpp) REVERT: A 166 MET cc_start: 0.8044 (mmm) cc_final: 0.7654 (mmt) REVERT: A 271 SER cc_start: 0.8816 (t) cc_final: 0.8500 (t) REVERT: B 102 MET cc_start: 0.8025 (mtm) cc_final: 0.7657 (mtp) REVERT: B 122 MET cc_start: 0.7936 (mmt) cc_final: 0.7349 (mmt) REVERT: B 166 MET cc_start: 0.7937 (mmm) cc_final: 0.7675 (mmp) REVERT: B 397 TRP cc_start: 0.8304 (m-10) cc_final: 0.8103 (m-10) REVERT: C 122 MET cc_start: 0.7814 (mmt) cc_final: 0.7334 (mmt) REVERT: C 129 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.7822 (mtm-85) REVERT: C 204 ARG cc_start: 0.8308 (tpt170) cc_final: 0.7523 (ttt180) REVERT: C 303 MET cc_start: 0.7332 (mpp) cc_final: 0.6737 (mtm) REVERT: D 122 MET cc_start: 0.7907 (mmt) cc_final: 0.7522 (tpp) REVERT: D 166 MET cc_start: 0.8063 (mmm) cc_final: 0.7663 (mmt) REVERT: D 271 SER cc_start: 0.8810 (t) cc_final: 0.8519 (t) REVERT: E 102 MET cc_start: 0.8045 (mtm) cc_final: 0.7673 (mtp) REVERT: E 122 MET cc_start: 0.7921 (mmt) cc_final: 0.7341 (mmt) REVERT: E 397 TRP cc_start: 0.8297 (m-10) cc_final: 0.8088 (m-10) REVERT: F 122 MET cc_start: 0.7764 (mmt) cc_final: 0.7247 (mmt) REVERT: F 129 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.7796 (mtm-85) REVERT: F 204 ARG cc_start: 0.8180 (tpt170) cc_final: 0.7436 (ttt180) REVERT: F 261 LEU cc_start: 0.7901 (pp) cc_final: 0.7633 (pp) REVERT: F 303 MET cc_start: 0.7557 (mpp) cc_final: 0.6757 (mtm) outliers start: 50 outliers final: 40 residues processed: 238 average time/residue: 0.1378 time to fit residues: 50.6211 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 : 0.686 ------------------------------------------------------------------------------- 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: 1.9990 chunk 46 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 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: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 GLN F 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.155540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.113880 restraints weight = 23437.107| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.73 r_work: 0.3365 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18972 Z= 0.136 Angle : 0.620 11.552 25668 Z= 0.290 Chirality : 0.043 0.210 3000 Planarity : 0.004 0.063 2904 Dihedral : 19.737 161.438 4308 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.15 % Allowed : 10.95 % Favored : 85.90 % 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: 1.93 (0.19), residues: 2142 helix: 2.38 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.41 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.010 0.001 TYR D 419 PHE 0.010 0.001 PHE D 177 TRP 0.009 0.001 TRP E 288 HIS 0.002 0.000 HIS C 401 Details of bonding type rmsd covalent geometry : bond 0.00306 (18960) covalent geometry : angle 0.61825 (25644) SS BOND : bond 0.00569 ( 12) SS BOND : angle 1.51939 ( 24) hydrogen bonds : bond 0.05187 ( 1182) hydrogen bonds : angle 3.15005 ( 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 259 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 200 time to evaluate : 0.660 Fit side-chains REVERT: A 122 MET cc_start: 0.7944 (mmt) cc_final: 0.7567 (tpp) REVERT: A 166 MET cc_start: 0.8283 (mmm) cc_final: 0.7793 (mmt) REVERT: A 271 SER cc_start: 0.8867 (t) cc_final: 0.8575 (t) REVERT: B 122 MET cc_start: 0.7948 (mmt) cc_final: 0.7432 (mmt) REVERT: B 166 MET cc_start: 0.8117 (mmm) cc_final: 0.7807 (mmp) REVERT: C 122 MET cc_start: 0.7852 (mmt) cc_final: 0.7389 (mmt) REVERT: C 129 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7813 (mtm-85) REVERT: C 204 ARG cc_start: 0.8289 (tpt170) cc_final: 0.7459 (ttt180) REVERT: C 303 MET cc_start: 0.7226 (mpp) cc_final: 0.6612 (mtm) REVERT: D 122 MET cc_start: 0.7936 (mmt) cc_final: 0.7539 (tpp) REVERT: D 166 MET cc_start: 0.8292 (mmm) cc_final: 0.7786 (mmt) REVERT: D 271 SER cc_start: 0.8871 (t) cc_final: 0.8572 (t) REVERT: E 122 MET cc_start: 0.7942 (mmt) cc_final: 0.7433 (mmt) REVERT: E 397 TRP cc_start: 0.8242 (m-10) cc_final: 0.8031 (m-10) REVERT: F 122 MET cc_start: 0.7800 (mmt) cc_final: 0.7306 (mmt) REVERT: F 129 ARG cc_start: 0.8299 (mmm-85) cc_final: 0.7819 (mtm-85) REVERT: F 204 ARG cc_start: 0.8198 (tpt170) cc_final: 0.7450 (ttt180) REVERT: F 303 MET cc_start: 0.7604 (mpp) cc_final: 0.6851 (mtm) outliers start: 59 outliers final: 45 residues processed: 239 average time/residue: 0.1413 time to fit residues: 52.2851 Evaluate side-chains 239 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 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 72 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 419 TYR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 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: 0.9980 chunk 140 optimal weight: 0.3980 chunk 65 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 0.0470 chunk 183 optimal weight: 0.9990 chunk 184 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.157734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116023 restraints weight = 23319.208| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.74 r_work: 0.3397 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18972 Z= 0.118 Angle : 0.579 11.056 25668 Z= 0.271 Chirality : 0.040 0.146 3000 Planarity : 0.003 0.052 2904 Dihedral : 18.706 160.943 4308 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.79 % Allowed : 10.36 % Favored : 85.84 % 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: 2.36 (0.19), residues: 2142 helix: 2.79 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.007 0.001 TYR C 395 PHE 0.009 0.001 PHE D 177 TRP 0.006 0.001 TRP F 140 HIS 0.002 0.000 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00259 (18960) covalent geometry : angle 0.57801 (25644) SS BOND : bond 0.00084 ( 12) SS BOND : angle 1.46929 ( 24) hydrogen bonds : bond 0.04624 ( 1182) hydrogen bonds : angle 3.01500 ( 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: 71 poor density : 218 time to evaluate : 0.677 Fit side-chains REVERT: A 122 MET cc_start: 0.7703 (mmt) cc_final: 0.7382 (tpp) REVERT: A 166 MET cc_start: 0.8195 (mmm) cc_final: 0.7719 (mmt) REVERT: A 190 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.6602 (m-70) REVERT: A 229 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7102 (t80) REVERT: A 261 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7194 (pp) REVERT: A 271 SER cc_start: 0.8828 (t) cc_final: 0.8534 (t) REVERT: B 122 MET cc_start: 0.7736 (mmt) cc_final: 0.7194 (mmt) REVERT: B 166 MET cc_start: 0.7981 (mmm) cc_final: 0.7624 (mmp) REVERT: B 258 ILE cc_start: 0.7905 (tt) cc_final: 0.7661 (tt) REVERT: B 261 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7612 (pp) REVERT: C 122 MET cc_start: 0.7600 (mmt) cc_final: 0.7090 (mmt) REVERT: C 129 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.7804 (mtm-85) REVERT: C 204 ARG cc_start: 0.8277 (tpt170) cc_final: 0.7390 (ttt180) REVERT: C 271 SER cc_start: 0.8497 (m) cc_final: 0.8213 (t) REVERT: C 303 MET cc_start: 0.7413 (mpp) cc_final: 0.6800 (mtm) REVERT: C 413 MET cc_start: 0.8819 (tpp) cc_final: 0.8376 (tpt) REVERT: D 122 MET cc_start: 0.7701 (mmt) cc_final: 0.7358 (tpp) REVERT: D 129 ARG cc_start: 0.8326 (mmm-85) cc_final: 0.7972 (mtm-85) REVERT: D 166 MET cc_start: 0.8208 (mmm) cc_final: 0.7719 (mmt) REVERT: D 190 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.6596 (m-70) REVERT: D 229 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7090 (t80) REVERT: D 271 SER cc_start: 0.8840 (t) cc_final: 0.8537 (t) REVERT: E 122 MET cc_start: 0.7723 (mmt) cc_final: 0.7214 (mmt) REVERT: E 258 ILE cc_start: 0.7918 (tt) cc_final: 0.7661 (tt) REVERT: E 261 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7633 (pp) REVERT: F 122 MET cc_start: 0.7578 (mmt) cc_final: 0.7080 (mmt) REVERT: F 129 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7808 (mtm-85) REVERT: F 204 ARG cc_start: 0.8217 (tpt170) cc_final: 0.7416 (ttt180) REVERT: F 271 SER cc_start: 0.8520 (m) cc_final: 0.8240 (t) REVERT: F 303 MET cc_start: 0.7497 (mpp) cc_final: 0.6874 (mtm) REVERT: F 413 MET cc_start: 0.8809 (tpp) cc_final: 0.8363 (tpt) outliers start: 71 outliers final: 46 residues processed: 269 average time/residue: 0.1429 time to fit residues: 59.2864 Evaluate side-chains 266 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 213 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 411 VAL Chi-restraints excluded: chain B residue 55 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 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 261 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 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain 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 411 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 25 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 15 optimal weight: 0.0040 chunk 130 optimal weight: 0.0370 chunk 179 optimal weight: 3.9990 overall best weight: 0.4670 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.159248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.117323 restraints weight = 23117.439| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.76 r_work: 0.3416 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18972 Z= 0.108 Angle : 0.566 10.840 25668 Z= 0.264 Chirality : 0.040 0.148 3000 Planarity : 0.004 0.079 2904 Dihedral : 17.896 159.461 4308 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.90 % Allowed : 11.11 % 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: 2.51 (0.19), residues: 2142 helix: 2.94 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.25 (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 A 177 TRP 0.006 0.001 TRP F 140 HIS 0.002 0.000 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00230 (18960) covalent geometry : angle 0.56579 (25644) SS BOND : bond 0.00146 ( 12) SS BOND : angle 0.98353 ( 24) hydrogen bonds : bond 0.04365 ( 1182) hydrogen bonds : angle 2.93820 ( 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 305 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 232 time to evaluate : 0.678 Fit side-chains REVERT: A 122 MET cc_start: 0.7675 (mmt) cc_final: 0.7343 (tpp) REVERT: A 129 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.7921 (mtm-85) REVERT: A 155 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7829 (tt) REVERT: A 166 MET cc_start: 0.8152 (mmm) cc_final: 0.7751 (tpp) REVERT: A 190 HIS cc_start: 0.7888 (OUTLIER) cc_final: 0.6620 (m-70) REVERT: A 229 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7132 (t80) REVERT: B 122 MET cc_start: 0.7707 (mmt) cc_final: 0.7125 (mmt) REVERT: B 155 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.8002 (tt) REVERT: B 166 MET cc_start: 0.7941 (mmm) cc_final: 0.7589 (mmp) REVERT: B 258 ILE cc_start: 0.7954 (tt) cc_final: 0.7723 (tt) REVERT: B 261 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7701 (pp) REVERT: B 268 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7532 (pp) REVERT: B 270 HIS cc_start: 0.7447 (p-80) cc_final: 0.7236 (p-80) REVERT: C 122 MET cc_start: 0.7497 (mmt) cc_final: 0.7002 (mmt) REVERT: C 129 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7839 (mtm-85) REVERT: C 155 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7821 (tt) REVERT: C 204 ARG cc_start: 0.8271 (tpt170) cc_final: 0.7436 (ttt180) REVERT: C 303 MET cc_start: 0.7399 (mpp) cc_final: 0.6866 (mtm) REVERT: D 122 MET cc_start: 0.7689 (mmt) cc_final: 0.7348 (tpp) REVERT: D 129 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.7932 (mtm-85) REVERT: D 155 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7833 (tt) REVERT: D 166 MET cc_start: 0.8172 (mmm) cc_final: 0.7756 (tpp) REVERT: D 190 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.6613 (m-70) REVERT: D 229 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7172 (t80) REVERT: D 271 SER cc_start: 0.8875 (t) cc_final: 0.8559 (t) REVERT: D 326 VAL cc_start: 0.7875 (OUTLIER) cc_final: 0.7634 (p) REVERT: E 122 MET cc_start: 0.7663 (mmt) cc_final: 0.7072 (mmt) REVERT: E 155 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.8015 (tt) REVERT: E 258 ILE cc_start: 0.7983 (tt) cc_final: 0.7742 (tt) REVERT: E 261 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7504 (pp) REVERT: E 268 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7607 (pp) REVERT: E 270 HIS cc_start: 0.7407 (p-80) cc_final: 0.7200 (p-80) REVERT: F 122 MET cc_start: 0.7462 (mmt) cc_final: 0.6975 (mmt) REVERT: F 129 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7824 (mtm-85) REVERT: F 155 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7821 (tt) REVERT: F 204 ARG cc_start: 0.8232 (tpt170) cc_final: 0.7404 (ttt180) REVERT: F 303 MET cc_start: 0.7348 (mpp) cc_final: 0.6789 (mtm) outliers start: 73 outliers final: 46 residues processed: 282 average time/residue: 0.1434 time to fit residues: 62.3196 Evaluate side-chains 279 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 218 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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 55 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 326 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 55 ILE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 326 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 185 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 70 optimal weight: 0.8980 chunk 195 optimal weight: 0.0980 chunk 145 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.157587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115818 restraints weight = 23445.781| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.76 r_work: 0.3395 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18972 Z= 0.119 Angle : 0.585 11.025 25668 Z= 0.274 Chirality : 0.040 0.150 3000 Planarity : 0.004 0.085 2904 Dihedral : 17.457 156.819 4308 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.58 % Allowed : 12.50 % Favored : 83.92 % 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: 2.59 (0.19), residues: 2142 helix: 2.98 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.008 0.001 TYR D 419 PHE 0.009 0.001 PHE D 304 TRP 0.006 0.001 TRP E 288 HIS 0.002 0.000 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00262 (18960) covalent geometry : angle 0.58445 (25644) SS BOND : bond 0.00158 ( 12) SS BOND : angle 0.98455 ( 24) hydrogen bonds : bond 0.04694 ( 1182) hydrogen bonds : angle 2.96164 ( 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 293 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 226 time to evaluate : 0.653 Fit side-chains REVERT: A 122 MET cc_start: 0.7821 (mmt) cc_final: 0.7471 (tpp) REVERT: A 129 ARG cc_start: 0.8383 (mmm-85) cc_final: 0.7942 (mtm-85) REVERT: A 155 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7854 (tt) REVERT: A 190 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.6635 (m-70) REVERT: A 229 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7308 (t80) REVERT: B 122 MET cc_start: 0.7762 (mmt) cc_final: 0.7434 (mmt) REVERT: B 155 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8100 (tt) REVERT: B 166 MET cc_start: 0.8063 (mmm) cc_final: 0.7685 (mmp) REVERT: B 258 ILE cc_start: 0.8017 (tt) cc_final: 0.7756 (tt) REVERT: B 261 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7749 (pp) REVERT: B 268 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7557 (pp) REVERT: B 270 HIS cc_start: 0.7341 (p-80) cc_final: 0.7124 (p-80) REVERT: C 122 MET cc_start: 0.7535 (mmt) cc_final: 0.7249 (mmt) REVERT: C 129 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.7831 (mtm-85) REVERT: C 155 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7847 (tt) REVERT: C 204 ARG cc_start: 0.8167 (tpt170) cc_final: 0.7204 (ttt180) REVERT: C 303 MET cc_start: 0.7395 (mpp) cc_final: 0.6866 (mtm) REVERT: D 122 MET cc_start: 0.7832 (mmt) cc_final: 0.7480 (tpp) REVERT: D 129 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7941 (mtm-85) REVERT: D 155 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7866 (tt) REVERT: D 190 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.6639 (m-70) REVERT: D 229 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7299 (t80) REVERT: E 122 MET cc_start: 0.7733 (mmt) cc_final: 0.7203 (mmt) REVERT: E 155 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8112 (tt) REVERT: E 258 ILE cc_start: 0.8011 (tt) cc_final: 0.7741 (tt) REVERT: E 261 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7609 (pp) REVERT: E 268 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7724 (pp) REVERT: E 270 HIS cc_start: 0.7307 (p-80) cc_final: 0.7090 (p-80) REVERT: F 122 MET cc_start: 0.7692 (mmt) cc_final: 0.7406 (mmt) REVERT: F 129 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7831 (mtm-85) REVERT: F 155 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7867 (tt) REVERT: F 204 ARG cc_start: 0.8273 (tpt170) cc_final: 0.7763 (ttt90) REVERT: F 303 MET cc_start: 0.7416 (mpp) cc_final: 0.6892 (mtm) outliers start: 67 outliers final: 50 residues processed: 272 average time/residue: 0.1452 time to fit residues: 60.6721 Evaluate side-chains 285 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 221 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 55 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 326 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 55 ILE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 326 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 200 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.154623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.113078 restraints weight = 23427.155| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.75 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: 0.7777 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18972 Z= 0.139 Angle : 0.613 11.299 25668 Z= 0.289 Chirality : 0.041 0.160 3000 Planarity : 0.004 0.085 2904 Dihedral : 17.138 152.720 4308 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.22 % Allowed : 12.02 % Favored : 83.76 % 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: 2.35 (0.19), residues: 2142 helix: 2.75 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -1.44 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.011 0.001 TYR D 419 PHE 0.010 0.001 PHE C 177 TRP 0.009 0.001 TRP B 288 HIS 0.002 0.000 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00323 (18960) covalent geometry : angle 0.61283 (25644) SS BOND : bond 0.00194 ( 12) SS BOND : angle 1.02465 ( 24) hydrogen bonds : bond 0.05315 ( 1182) hydrogen bonds : angle 3.06753 ( 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 289 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 210 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8020 (mmt) cc_final: 0.7454 (mmt) REVERT: A 129 ARG cc_start: 0.8399 (mmm-85) cc_final: 0.7949 (mtm-85) REVERT: A 229 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7356 (t80) REVERT: B 122 MET cc_start: 0.8092 (mmt) cc_final: 0.7761 (mmt) REVERT: B 155 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8132 (tt) REVERT: B 166 MET cc_start: 0.8321 (mmm) cc_final: 0.7967 (mmp) REVERT: B 258 ILE cc_start: 0.8073 (tt) cc_final: 0.7853 (tt) REVERT: B 261 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7797 (pp) REVERT: B 268 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7583 (pp) REVERT: B 270 HIS cc_start: 0.7385 (p-80) cc_final: 0.7145 (p-80) REVERT: C 122 MET cc_start: 0.7993 (mmt) cc_final: 0.7733 (mmt) REVERT: C 129 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7775 (mtm-85) REVERT: C 155 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7889 (tt) REVERT: C 204 ARG cc_start: 0.8162 (tpt170) cc_final: 0.7570 (ttt90) REVERT: C 303 MET cc_start: 0.7389 (mpp) cc_final: 0.6931 (mtm) REVERT: D 122 MET cc_start: 0.8028 (mmt) cc_final: 0.7453 (mmt) REVERT: D 129 ARG cc_start: 0.8360 (mmm-85) cc_final: 0.7951 (mtm-85) REVERT: D 155 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.8032 (mt) REVERT: D 190 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.6611 (m-70) REVERT: D 229 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7359 (t80) REVERT: E 122 MET cc_start: 0.7999 (mmt) cc_final: 0.7460 (mmt) REVERT: E 155 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8147 (tt) REVERT: E 206 TYR cc_start: 0.5922 (m-10) cc_final: 0.5590 (m-10) REVERT: E 258 ILE cc_start: 0.8067 (tt) cc_final: 0.7758 (tt) REVERT: E 261 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7593 (pp) REVERT: E 268 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7739 (pp) REVERT: F 122 MET cc_start: 0.7966 (mmt) cc_final: 0.7752 (mmt) REVERT: F 129 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7775 (mtm-85) REVERT: F 155 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7909 (tt) REVERT: F 204 ARG cc_start: 0.8216 (tpt170) cc_final: 0.7717 (ttt90) REVERT: F 303 MET cc_start: 0.7424 (mpp) cc_final: 0.6994 (mtm) outliers start: 79 outliers final: 55 residues processed: 266 average time/residue: 0.1436 time to fit residues: 58.7934 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 : 0.584 ------------------------------------------------------------------------------- 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 229 TYR 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 126 LYS Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 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 126 LYS Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 326 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 8 optimal weight: 0.1980 chunk 82 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 203 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.4057 r_free = 0.4057 target = 0.155841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114408 restraints weight = 23415.443| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.73 r_work: 0.3374 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18972 Z= 0.125 Angle : 0.603 10.945 25668 Z= 0.283 Chirality : 0.040 0.153 3000 Planarity : 0.004 0.087 2904 Dihedral : 16.845 150.922 4308 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.90 % Allowed : 12.34 % Favored : 83.76 % 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: 2.66 (0.19), residues: 2142 helix: 3.05 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.20 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.011 0.001 TYR D 97 PHE 0.009 0.001 PHE A 304 TRP 0.007 0.001 TRP D 418 HIS 0.002 0.000 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00281 (18960) covalent geometry : angle 0.60207 (25644) SS BOND : bond 0.00191 ( 12) SS BOND : angle 1.32516 ( 24) hydrogen bonds : bond 0.04869 ( 1182) hydrogen bonds : angle 3.00493 ( 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 283 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 210 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.7760 (mmt) cc_final: 0.7432 (tpp) REVERT: A 129 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.7930 (mtm-85) REVERT: A 190 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.6548 (m-70) REVERT: A 229 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7370 (t80) REVERT: B 122 MET cc_start: 0.7895 (mmt) cc_final: 0.7579 (mmt) REVERT: B 155 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8075 (tt) REVERT: B 166 MET cc_start: 0.8231 (mmm) cc_final: 0.7895 (mmp) REVERT: B 206 TYR cc_start: 0.5861 (m-10) cc_final: 0.5517 (m-10) REVERT: B 258 ILE cc_start: 0.8019 (tt) cc_final: 0.7721 (tt) REVERT: B 261 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7670 (pp) REVERT: B 268 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7534 (pp) REVERT: B 270 HIS cc_start: 0.7348 (p-80) cc_final: 0.7114 (p-80) REVERT: C 122 MET cc_start: 0.7767 (mmt) cc_final: 0.7539 (mmt) REVERT: C 129 ARG cc_start: 0.8250 (mmm-85) cc_final: 0.7756 (mtm-85) REVERT: C 155 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7826 (tt) REVERT: C 204 ARG cc_start: 0.8132 (tpt170) cc_final: 0.7540 (ttt90) REVERT: C 303 MET cc_start: 0.7488 (mpp) cc_final: 0.7111 (mtm) REVERT: D 122 MET cc_start: 0.7774 (mmt) cc_final: 0.7446 (tpp) REVERT: D 129 ARG cc_start: 0.8406 (mmm-85) cc_final: 0.7998 (mtm-85) REVERT: D 155 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7955 (mt) REVERT: D 190 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.6548 (m-70) REVERT: D 229 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7370 (t80) REVERT: E 122 MET cc_start: 0.7767 (mmt) cc_final: 0.7261 (mmt) REVERT: E 155 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8098 (tt) REVERT: E 206 TYR cc_start: 0.5932 (m-10) cc_final: 0.5655 (m-10) REVERT: E 258 ILE cc_start: 0.8031 (tt) cc_final: 0.7725 (tt) REVERT: E 261 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7531 (pp) REVERT: E 268 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7706 (pp) REVERT: E 270 HIS cc_start: 0.7335 (p-80) cc_final: 0.7096 (p-80) REVERT: F 122 MET cc_start: 0.7751 (mmt) cc_final: 0.7530 (mmt) REVERT: F 129 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7752 (mtm-85) REVERT: F 155 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7851 (tt) REVERT: F 204 ARG cc_start: 0.8191 (tpt170) cc_final: 0.7696 (ttt90) REVERT: F 303 MET cc_start: 0.7431 (mpp) cc_final: 0.7040 (mtm) outliers start: 73 outliers final: 55 residues processed: 263 average time/residue: 0.1446 time to fit residues: 59.0494 Evaluate side-chains 278 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 210 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 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 126 LYS Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 95 CYS 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 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 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 130 ASP Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 95 CYS 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 180 optimal weight: 0.3980 chunk 183 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 184 optimal weight: 0.3980 chunk 8 optimal weight: 0.0060 chunk 53 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.158511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.117024 restraints weight = 23175.800| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.73 r_work: 0.3416 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18972 Z= 0.111 Angle : 0.584 10.634 25668 Z= 0.274 Chirality : 0.040 0.154 3000 Planarity : 0.004 0.085 2904 Dihedral : 16.495 148.375 4308 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.58 % Allowed : 12.77 % Favored : 83.65 % 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: 2.75 (0.19), residues: 2142 helix: 3.15 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.23 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.013 0.001 TYR A 97 PHE 0.009 0.001 PHE A 304 TRP 0.006 0.001 TRP C 140 HIS 0.002 0.000 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00239 (18960) covalent geometry : angle 0.58308 (25644) SS BOND : bond 0.00198 ( 12) SS BOND : angle 1.38402 ( 24) hydrogen bonds : bond 0.04318 ( 1182) hydrogen bonds : angle 2.92725 ( 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 302 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 235 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.7636 (mmt) cc_final: 0.7328 (tpp) REVERT: A 129 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.7945 (mtm-85) REVERT: A 190 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.6571 (m-70) REVERT: A 229 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7404 (t80) REVERT: B 122 MET cc_start: 0.7740 (mmt) cc_final: 0.7441 (mmt) REVERT: B 155 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7997 (tt) REVERT: B 166 MET cc_start: 0.8002 (mmm) cc_final: 0.7651 (mmp) REVERT: B 206 TYR cc_start: 0.5705 (m-10) cc_final: 0.5377 (m-10) REVERT: B 258 ILE cc_start: 0.7934 (tt) cc_final: 0.7651 (tt) REVERT: B 261 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7648 (pp) REVERT: B 268 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7518 (pp) REVERT: B 270 HIS cc_start: 0.7333 (p-80) cc_final: 0.7131 (p-80) REVERT: B 451 TRP cc_start: 0.7707 (t-100) cc_final: 0.7068 (t60) REVERT: C 122 MET cc_start: 0.7595 (mmt) cc_final: 0.7336 (mmt) REVERT: C 129 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.7811 (mtm-85) REVERT: C 155 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7773 (tt) REVERT: C 159 ASP cc_start: 0.8085 (t70) cc_final: 0.7825 (p0) REVERT: C 204 ARG cc_start: 0.8098 (tpt170) cc_final: 0.7505 (ttt90) REVERT: C 303 MET cc_start: 0.7472 (mpp) cc_final: 0.7124 (mtm) REVERT: D 122 MET cc_start: 0.7656 (mmt) cc_final: 0.7355 (tpp) REVERT: D 129 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.7995 (mtm-85) REVERT: D 155 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7788 (tt) REVERT: D 190 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.6496 (m-70) REVERT: D 229 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7352 (t80) REVERT: E 122 MET cc_start: 0.7640 (mmt) cc_final: 0.7059 (mmt) REVERT: E 206 TYR cc_start: 0.6049 (m-10) cc_final: 0.5798 (m-10) REVERT: E 258 ILE cc_start: 0.7979 (tt) cc_final: 0.7696 (tt) REVERT: E 261 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7499 (pp) REVERT: E 268 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7613 (pp) REVERT: E 270 HIS cc_start: 0.7336 (p-80) cc_final: 0.7134 (p-80) REVERT: E 451 TRP cc_start: 0.7736 (t-100) cc_final: 0.7066 (t60) REVERT: F 122 MET cc_start: 0.7592 (mmt) cc_final: 0.7335 (mmt) REVERT: F 129 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7758 (mtm-85) REVERT: F 155 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7792 (tt) REVERT: F 204 ARG cc_start: 0.8158 (tpt170) cc_final: 0.7665 (ttt90) REVERT: F 303 MET cc_start: 0.7506 (mpp) cc_final: 0.7143 (mtm) outliers start: 67 outliers final: 52 residues processed: 276 average time/residue: 0.1406 time to fit residues: 59.6861 Evaluate side-chains 296 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 232 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 264 VAL 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 126 LYS Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 95 CYS 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 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 55 ILE 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 95 CYS 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: 0.0000 chunk 130 optimal weight: 0.0870 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 87 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 124 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.2038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 HIS E 136 GLN E 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.164635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.122637 restraints weight = 23129.863| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.77 r_work: 0.3503 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18972 Z= 0.102 Angle : 0.570 10.249 25668 Z= 0.266 Chirality : 0.039 0.145 3000 Planarity : 0.004 0.082 2904 Dihedral : 16.001 147.869 4308 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.31 % Allowed : 13.09 % Favored : 83.60 % 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: 2.76 (0.19), residues: 2142 helix: 3.16 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -1.38 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 39 TYR 0.009 0.001 TYR A 97 PHE 0.009 0.001 PHE A 304 TRP 0.007 0.001 TRP F 140 HIS 0.004 0.000 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00212 (18960) covalent geometry : angle 0.56900 (25644) SS BOND : bond 0.00178 ( 12) SS BOND : angle 1.44579 ( 24) hydrogen bonds : bond 0.03509 ( 1182) hydrogen bonds : angle 2.81973 ( 3456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3598.90 seconds wall clock time: 63 minutes 6.18 seconds (3786.18 seconds total)