Starting phenix.real_space_refine on Fri Jul 3 15:14:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m6n_23701/07_2026/7m6n_23701.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6n_23701/07_2026/7m6n_23701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m6n_23701/07_2026/7m6n_23701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6n_23701/07_2026/7m6n_23701.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7m6n_23701/07_2026/7m6n_23701.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m6n_23701/07_2026/7m6n_23701.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6n_23701/07_2026/7m6n_23701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6n_23701/07_2026/7m6n_23701.map" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9540 2.51 5 N 2410 2.21 5 O 2650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14700 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2921 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2921 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2921 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2921 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2921 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.38, per 1000 atoms: 0.16 Number of scatterers: 14700 At special positions: 0 Unit cell: (94.6, 93.5, 138.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2650 8.00 N 2410 7.00 C 9540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 176 " distance=2.04 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 176 " distance=2.04 Simple disulfide: pdb=" SG CYS E 162 " - pdb=" SG CYS E 176 " distance=2.04 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 176 " distance=2.04 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 176 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 802 " - " ASN A 62 " " NAG B 802 " - " ASN B 62 " " NAG C 802 " - " ASN C 62 " " NAG D 802 " - " ASN D 62 " " NAG E 802 " - " ASN E 62 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 468.1 milliseconds 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 25 sheets defined 41.7% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.993A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 removed outlier: 3.713A pdb=" N MET A 113 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 252 removed outlier: 3.684A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 269 removed outlier: 4.190A pdb=" N SER A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP A 267 " --> pdb=" O TRP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 295 removed outlier: 3.689A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 341 removed outlier: 3.851A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 444 removed outlier: 4.305A pdb=" N MET A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 4.544A pdb=" N ILE A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N HIS A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 43 removed outlier: 3.993A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.711A pdb=" N MET D 113 " --> pdb=" O ASP D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 removed outlier: 3.684A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 269 removed outlier: 4.191A pdb=" N SER D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP D 267 " --> pdb=" O TRP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 295 removed outlier: 3.689A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 341 removed outlier: 3.851A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 444 removed outlier: 4.304A pdb=" N MET D 399 " --> pdb=" O THR D 395 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 400 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 4.543A pdb=" N ILE D 441 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N HIS D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 43 removed outlier: 3.993A pdb=" N PHE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 114 removed outlier: 3.712A pdb=" N MET E 113 " --> pdb=" O ASP E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 removed outlier: 3.684A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 269 removed outlier: 4.190A pdb=" N SER E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 295 removed outlier: 3.690A pdb=" N ARG E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 341 removed outlier: 3.851A pdb=" N PHE E 341 " --> pdb=" O GLU E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 444 removed outlier: 4.305A pdb=" N MET E 399 " --> pdb=" O THR E 395 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG E 400 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Proline residue: E 419 - end of helix removed outlier: 4.544A pdb=" N ILE E 441 " --> pdb=" O ARG E 437 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N HIS E 442 " --> pdb=" O SER E 438 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS E 443 " --> pdb=" O GLU E 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 43 removed outlier: 3.992A pdb=" N PHE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.712A pdb=" N MET B 113 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 removed outlier: 3.683A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 269 removed outlier: 4.190A pdb=" N SER B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP B 267 " --> pdb=" O TRP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 295 removed outlier: 3.689A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 341 removed outlier: 3.851A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 444 removed outlier: 4.306A pdb=" N MET B 399 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 4.543A pdb=" N ILE B 441 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N HIS B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 43 removed outlier: 3.993A pdb=" N PHE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 114 removed outlier: 3.712A pdb=" N MET C 113 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.684A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 269 removed outlier: 4.190A pdb=" N SER C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE C 266 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP C 267 " --> pdb=" O TRP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 295 removed outlier: 3.689A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 341 removed outlier: 3.851A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 444 removed outlier: 4.305A pdb=" N MET C 399 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG C 400 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 4.545A pdb=" N ILE C 441 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N HIS C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.543A pdb=" N ILE A 144 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 142 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 5.639A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'D' and resid 107 through 109 removed outlier: 3.542A pdb=" N ILE D 144 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU D 142 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 127 through 132 removed outlier: 5.639A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 122 through 124 Processing sheet with id=AA9, first strand: chain 'D' and resid 122 through 124 Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'E' and resid 107 through 109 removed outlier: 3.542A pdb=" N ILE E 144 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU E 142 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 127 through 132 removed outlier: 5.639A pdb=" N VAL E 159 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE E 132 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N ARG E 155 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 122 through 124 Processing sheet with id=AB5, first strand: chain 'E' and resid 122 through 124 Processing sheet with id=AB6, first strand: chain 'E' and resid 224 through 225 Processing sheet with id=AB7, first strand: chain 'B' and resid 107 through 109 removed outlier: 3.542A pdb=" N ILE B 144 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 127 through 132 removed outlier: 5.639A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AC1, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AC2, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AC3, first strand: chain 'C' and resid 107 through 109 removed outlier: 3.543A pdb=" N ILE C 144 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU C 142 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 127 through 132 removed outlier: 5.639A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 122 through 124 Processing sheet with id=AC6, first strand: chain 'C' and resid 122 through 124 Processing sheet with id=AC7, first strand: chain 'C' and resid 224 through 225 890 hydrogen bonds defined for protein. 2625 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: 2.59 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4173 1.34 - 1.46: 3392 1.46 - 1.58: 7315 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 15050 Sorted by residual: bond pdb=" CG LEU E 190 " pdb=" CD2 LEU E 190 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.54e+00 bond pdb=" CG LEU D 190 " pdb=" CD2 LEU D 190 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.51e+00 bond pdb=" CG LEU C 190 " pdb=" CD2 LEU C 190 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.50e+00 bond pdb=" CG LEU B 190 " pdb=" CD2 LEU B 190 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.49e+00 bond pdb=" CG LEU A 190 " pdb=" CD2 LEU A 190 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.49e+00 ... (remaining 15045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 18591 2.07 - 4.13: 1482 4.13 - 6.20: 226 6.20 - 8.26: 73 8.26 - 10.33: 23 Bond angle restraints: 20395 Sorted by residual: angle pdb=" C PHE B 266 " pdb=" CA PHE B 266 " pdb=" CB PHE B 266 " ideal model delta sigma weight residual 110.85 104.16 6.69 1.70e+00 3.46e-01 1.55e+01 angle pdb=" C PHE A 266 " pdb=" CA PHE A 266 " pdb=" CB PHE A 266 " ideal model delta sigma weight residual 110.85 104.17 6.68 1.70e+00 3.46e-01 1.54e+01 angle pdb=" C PHE C 266 " pdb=" CA PHE C 266 " pdb=" CB PHE C 266 " ideal model delta sigma weight residual 110.85 104.17 6.68 1.70e+00 3.46e-01 1.54e+01 angle pdb=" C PHE E 266 " pdb=" CA PHE E 266 " pdb=" CB PHE E 266 " ideal model delta sigma weight residual 110.85 104.19 6.66 1.70e+00 3.46e-01 1.54e+01 angle pdb=" C PHE D 266 " pdb=" CA PHE D 266 " pdb=" CB PHE D 266 " ideal model delta sigma weight residual 110.85 104.21 6.64 1.70e+00 3.46e-01 1.53e+01 ... (remaining 20390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 8333 16.67 - 33.34: 503 33.34 - 50.02: 114 50.02 - 66.69: 20 66.69 - 83.36: 5 Dihedral angle restraints: 8975 sinusoidal: 3635 harmonic: 5340 Sorted by residual: dihedral pdb=" CA MET B 42 " pdb=" C MET B 42 " pdb=" N GLY B 43 " pdb=" CA GLY B 43 " ideal model delta harmonic sigma weight residual 180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA MET D 42 " pdb=" C MET D 42 " pdb=" N GLY D 43 " pdb=" CA GLY D 43 " ideal model delta harmonic sigma weight residual -180.00 -153.84 -26.16 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA MET A 42 " pdb=" C MET A 42 " pdb=" N GLY A 43 " pdb=" CA GLY A 43 " ideal model delta harmonic sigma weight residual -180.00 -153.84 -26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 8972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1486 0.067 - 0.134: 581 0.134 - 0.201: 167 0.201 - 0.268: 53 0.268 - 0.335: 13 Chirality restraints: 2300 Sorted by residual: chirality pdb=" CB THR E 157 " pdb=" CA THR E 157 " pdb=" OG1 THR E 157 " pdb=" CG2 THR E 157 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB THR C 157 " pdb=" CA THR C 157 " pdb=" OG1 THR C 157 " pdb=" CG2 THR C 157 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB THR A 157 " pdb=" CA THR A 157 " pdb=" OG1 THR A 157 " pdb=" CG2 THR A 157 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 2297 not shown) Planarity restraints: 2560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 279 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C LEU C 279 " 0.063 2.00e-02 2.50e+03 pdb=" O LEU C 279 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY C 280 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 279 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C LEU E 279 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU E 279 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY E 280 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 279 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.34e+01 pdb=" C LEU B 279 " 0.063 2.00e-02 2.50e+03 pdb=" O LEU B 279 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY B 280 " -0.021 2.00e-02 2.50e+03 ... (remaining 2557 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1921 2.76 - 3.30: 14112 3.30 - 3.83: 24009 3.83 - 4.37: 28780 4.37 - 4.90: 49370 Nonbonded interactions: 118192 Sorted by model distance: nonbonded pdb=" O LEU A 122 " pdb=" OG1 THR B 136 " model vdw 2.228 3.040 nonbonded pdb=" O LEU D 122 " pdb=" OG1 THR E 136 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR A 136 " pdb=" O LEU E 122 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR D 136 " pdb=" O LEU C 122 " model vdw 2.319 3.040 nonbonded pdb=" OD2 ASP C 110 " pdb=" OG SER C 112 " model vdw 2.319 3.040 ... (remaining 118187 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'B' selection = chain 'C' } 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: 1.620 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.700 Find NCS groups from input model: 0.130 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:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 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 : 0.009 0.096 15060 Z= 0.390 Angle : 1.281 10.328 20420 Z= 0.721 Chirality : 0.081 0.335 2300 Planarity : 0.009 0.055 2555 Dihedral : 11.946 83.360 5490 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.31 % Allowed : 2.99 % Favored : 96.70 % 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: 0.23 (0.19), residues: 1785 helix: 1.80 (0.18), residues: 600 sheet: 0.92 (0.29), residues: 375 loop : -1.58 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG E 220 TYR 0.060 0.005 TYR A 433 PHE 0.052 0.006 PHE B 87 TRP 0.023 0.003 TRP E 263 HIS 0.007 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00867 / 0.39 (15050) covalent geometry : angle 1.27891 / 0.72 (20395) SS BOND : bond 0.00984 / 0.58 ( 5) SS BOND : angle 1.43996 / 0.78 ( 10) hydrogen bonds : bond 0.16123 / 10.57 ( 745) hydrogen bonds : angle 6.97728 / 4.86 ( 2625) link_NAG-ASN : bond 0.00541 / 0.31 ( 5) link_NAG-ASN : angle 2.85276 / 1.58 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 215 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8582 (mmm) cc_final: 0.8336 (mmm) REVERT: A 263 TRP cc_start: 0.8179 (m-10) cc_final: 0.7635 (m-10) REVERT: B 187 MET cc_start: 0.8609 (mmm) cc_final: 0.8332 (mmm) REVERT: C 178 MET cc_start: 0.8119 (ttm) cc_final: 0.7827 (ttp) REVERT: C 187 MET cc_start: 0.8544 (mmm) cc_final: 0.8277 (mmm) REVERT: C 263 TRP cc_start: 0.8292 (m-10) cc_final: 0.8056 (m-10) outliers start: 5 outliers final: 3 residues processed: 215 average time/residue: 0.5018 time to fit residues: 118.7265 Evaluate side-chains 119 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain C residue 115 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 334 GLN ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 ASN D 334 GLN ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 ASN E 334 GLN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN C 334 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.092973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.070360 restraints weight = 34366.094| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.16 r_work: 0.3022 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15060 Z= 0.160 Angle : 0.663 9.545 20420 Z= 0.353 Chirality : 0.045 0.164 2300 Planarity : 0.005 0.050 2555 Dihedral : 4.977 20.466 1971 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.12 % Allowed : 10.90 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1785 helix: 2.45 (0.19), residues: 660 sheet: 1.05 (0.27), residues: 380 loop : -1.38 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 242 TYR 0.026 0.002 TYR E 433 PHE 0.023 0.002 PHE C 87 TRP 0.011 0.002 TRP A 263 HIS 0.002 0.000 HIS E 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (15050) covalent geometry : angle 0.66251 / 0.35 (20395) SS BOND : bond 0.00475 / 0.28 ( 5) SS BOND : angle 0.55112 / 0.29 ( 10) hydrogen bonds : bond 0.05239 / 3.47 ( 745) hydrogen bonds : angle 5.09650 / 3.60 ( 2625) link_NAG-ASN : bond 0.00254 / 0.15 ( 5) link_NAG-ASN : angle 1.29035 / 0.70 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8968 (mmm) cc_final: 0.8600 (mmm) REVERT: A 263 TRP cc_start: 0.8134 (m-10) cc_final: 0.7690 (m-10) REVERT: D 113 MET cc_start: 0.8576 (ppp) cc_final: 0.8245 (pp-130) REVERT: E 113 MET cc_start: 0.8569 (ppp) cc_final: 0.8025 (ppp) REVERT: E 221 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7716 (p90) REVERT: B 187 MET cc_start: 0.8981 (mmm) cc_final: 0.8586 (mmm) REVERT: C 178 MET cc_start: 0.9387 (ttm) cc_final: 0.9102 (ttp) REVERT: C 187 MET cc_start: 0.8979 (mmm) cc_final: 0.8347 (mmm) outliers start: 18 outliers final: 4 residues processed: 135 average time/residue: 0.4702 time to fit residues: 70.5636 Evaluate side-chains 108 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 188 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.091356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068644 restraints weight = 34921.247| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.20 r_work: 0.2976 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15060 Z= 0.163 Angle : 0.610 8.260 20420 Z= 0.322 Chirality : 0.044 0.152 2300 Planarity : 0.004 0.036 2555 Dihedral : 5.041 56.895 1967 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.81 % Allowed : 11.21 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.20), residues: 1785 helix: 2.62 (0.19), residues: 655 sheet: 1.03 (0.27), residues: 390 loop : -1.53 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 333 TYR 0.025 0.002 TYR A 433 PHE 0.035 0.002 PHE D 330 TRP 0.009 0.001 TRP C 263 HIS 0.003 0.001 HIS B 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (15050) covalent geometry : angle 0.60910 / 0.32 (20395) SS BOND : bond 0.00415 / 0.24 ( 5) SS BOND : angle 0.47775 / 0.24 ( 10) hydrogen bonds : bond 0.04721 / 3.12 ( 745) hydrogen bonds : angle 4.86507 / 3.46 ( 2625) link_NAG-ASN : bond 0.00133 / 0.08 ( 5) link_NAG-ASN : angle 1.42029 / 0.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9039 (mmm) cc_final: 0.8647 (mmm) REVERT: A 263 TRP cc_start: 0.7969 (m-10) cc_final: 0.7561 (m-10) REVERT: D 113 MET cc_start: 0.8595 (ppp) cc_final: 0.8238 (pp-130) REVERT: D 221 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7683 (p90) REVERT: D 270 MET cc_start: 0.6693 (tmt) cc_final: 0.6433 (ppp) REVERT: E 113 MET cc_start: 0.8562 (ppp) cc_final: 0.8007 (ppp) REVERT: E 221 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7675 (p90) REVERT: B 187 MET cc_start: 0.9040 (mmm) cc_final: 0.8692 (mmm) REVERT: B 221 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7625 (p90) REVERT: C 178 MET cc_start: 0.9411 (ttm) cc_final: 0.9090 (ttp) REVERT: C 187 MET cc_start: 0.8960 (mmm) cc_final: 0.8405 (mmm) outliers start: 29 outliers final: 4 residues processed: 126 average time/residue: 0.5278 time to fit residues: 73.6437 Evaluate side-chains 109 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 188 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 0.0000 chunk 141 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.090800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067889 restraints weight = 34706.876| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.19 r_work: 0.2963 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15060 Z= 0.155 Angle : 0.586 8.033 20420 Z= 0.308 Chirality : 0.043 0.151 2300 Planarity : 0.003 0.035 2555 Dihedral : 4.822 21.859 1965 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.55 % Allowed : 11.40 % Favored : 86.04 % 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: 0.97 (0.20), residues: 1785 helix: 2.63 (0.19), residues: 655 sheet: 1.04 (0.27), residues: 390 loop : -1.54 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.024 0.002 TYR A 433 PHE 0.032 0.002 PHE A 330 TRP 0.012 0.001 TRP C 263 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (15050) covalent geometry : angle 0.58569 / 0.31 (20395) SS BOND : bond 0.00354 / 0.21 ( 5) SS BOND : angle 0.41325 / 0.22 ( 10) hydrogen bonds : bond 0.04367 / 2.91 ( 745) hydrogen bonds : angle 4.74824 / 3.39 ( 2625) link_NAG-ASN : bond 0.00142 / 0.08 ( 5) link_NAG-ASN : angle 1.20742 / 0.66 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9077 (mmm) cc_final: 0.8665 (mmm) REVERT: A 263 TRP cc_start: 0.7935 (m-10) cc_final: 0.7320 (m-10) REVERT: D 113 MET cc_start: 0.8604 (ppp) cc_final: 0.8043 (ppp) REVERT: D 221 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7627 (p90) REVERT: E 113 MET cc_start: 0.8648 (ppp) cc_final: 0.8123 (ppp) REVERT: E 221 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7650 (p90) REVERT: B 187 MET cc_start: 0.9091 (mmm) cc_final: 0.8668 (mmm) REVERT: B 221 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7672 (p90) REVERT: C 178 MET cc_start: 0.9445 (ttm) cc_final: 0.9125 (ttp) REVERT: C 187 MET cc_start: 0.9042 (mmm) cc_final: 0.8440 (mmm) outliers start: 41 outliers final: 13 residues processed: 138 average time/residue: 0.4545 time to fit residues: 70.0709 Evaluate side-chains 118 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 119 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 47 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 0.0670 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.091496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068582 restraints weight = 34812.021| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.19 r_work: 0.2976 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15060 Z= 0.126 Angle : 0.570 8.717 20420 Z= 0.296 Chirality : 0.042 0.151 2300 Planarity : 0.003 0.033 2555 Dihedral : 4.687 21.896 1965 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.24 % Allowed : 11.90 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1785 helix: 2.75 (0.19), residues: 625 sheet: 0.98 (0.27), residues: 390 loop : -1.62 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 242 TYR 0.021 0.002 TYR A 433 PHE 0.039 0.001 PHE E 330 TRP 0.030 0.001 TRP A 267 HIS 0.002 0.000 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (15050) covalent geometry : angle 0.56926 / 0.30 (20395) SS BOND : bond 0.00292 / 0.17 ( 5) SS BOND : angle 0.26125 / 0.14 ( 10) hydrogen bonds : bond 0.04088 / 2.73 ( 745) hydrogen bonds : angle 4.62401 / 3.31 ( 2625) link_NAG-ASN : bond 0.00213 / 0.12 ( 5) link_NAG-ASN : angle 0.98715 / 0.54 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8495 (pp-130) cc_final: 0.7919 (ppp) REVERT: A 187 MET cc_start: 0.9093 (mmm) cc_final: 0.8775 (mmm) REVERT: A 263 TRP cc_start: 0.7793 (m-10) cc_final: 0.7375 (m-10) REVERT: A 334 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6889 (mp10) REVERT: D 113 MET cc_start: 0.8662 (ppp) cc_final: 0.8266 (pp-130) REVERT: D 221 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7576 (p90) REVERT: D 270 MET cc_start: 0.6704 (tmt) cc_final: 0.6491 (ppp) REVERT: E 113 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8116 (ppp) REVERT: E 221 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7617 (p90) REVERT: B 187 MET cc_start: 0.9103 (mmm) cc_final: 0.8658 (mmm) REVERT: B 221 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7661 (p90) REVERT: C 178 MET cc_start: 0.9431 (ttm) cc_final: 0.9091 (ttp) REVERT: C 187 MET cc_start: 0.9068 (mmm) cc_final: 0.8543 (mmm) outliers start: 36 outliers final: 13 residues processed: 133 average time/residue: 0.5172 time to fit residues: 76.0389 Evaluate side-chains 125 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 188 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 3 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 0.0770 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.091823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.068909 restraints weight = 34622.043| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.20 r_work: 0.2982 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15060 Z= 0.127 Angle : 0.562 8.289 20420 Z= 0.292 Chirality : 0.042 0.149 2300 Planarity : 0.003 0.032 2555 Dihedral : 4.596 22.219 1965 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.06 % Allowed : 12.90 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1785 helix: 2.78 (0.19), residues: 625 sheet: 0.90 (0.26), residues: 390 loop : -1.58 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 415 TYR 0.019 0.002 TYR B 433 PHE 0.034 0.001 PHE B 330 TRP 0.025 0.001 TRP A 267 HIS 0.002 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (15050) covalent geometry : angle 0.56133 / 0.29 (20395) SS BOND : bond 0.00285 / 0.17 ( 5) SS BOND : angle 0.26049 / 0.13 ( 10) hydrogen bonds : bond 0.03948 / 2.64 ( 745) hydrogen bonds : angle 4.55066 / 3.26 ( 2625) link_NAG-ASN : bond 0.00181 / 0.10 ( 5) link_NAG-ASN : angle 1.01362 / 0.56 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8414 (pp-130) cc_final: 0.8146 (ppp) REVERT: A 187 MET cc_start: 0.9170 (mmm) cc_final: 0.8817 (mmm) REVERT: A 263 TRP cc_start: 0.7752 (m-10) cc_final: 0.7348 (m-10) REVERT: A 334 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6932 (mp10) REVERT: D 113 MET cc_start: 0.8605 (ppp) cc_final: 0.7960 (ppp) REVERT: D 221 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7638 (p90) REVERT: D 270 MET cc_start: 0.6707 (tmt) cc_final: 0.6494 (ppp) REVERT: D 334 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6859 (mp10) REVERT: E 113 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8110 (ppp) REVERT: E 221 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7572 (p90) REVERT: B 187 MET cc_start: 0.9101 (mmm) cc_final: 0.8737 (mmm) REVERT: B 221 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.7695 (p90) REVERT: C 187 MET cc_start: 0.9064 (mmm) cc_final: 0.8499 (mmm) outliers start: 33 outliers final: 13 residues processed: 135 average time/residue: 0.4881 time to fit residues: 73.2434 Evaluate side-chains 130 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 334 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 428 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 145 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.066337 restraints weight = 34701.206| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.18 r_work: 0.2924 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15060 Z= 0.187 Angle : 0.611 8.283 20420 Z= 0.317 Chirality : 0.043 0.147 2300 Planarity : 0.003 0.032 2555 Dihedral : 4.806 23.904 1965 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.31 % Allowed : 13.46 % Favored : 84.24 % 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: 0.82 (0.20), residues: 1785 helix: 2.72 (0.19), residues: 625 sheet: 0.75 (0.27), residues: 395 loop : -1.54 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 242 TYR 0.025 0.002 TYR B 433 PHE 0.024 0.002 PHE B 330 TRP 0.015 0.001 TRP E 267 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (15050) covalent geometry : angle 0.61024 / 0.32 (20395) SS BOND : bond 0.00340 / 0.20 ( 5) SS BOND : angle 0.55828 / 0.28 ( 10) hydrogen bonds : bond 0.04282 / 2.85 ( 745) hydrogen bonds : angle 4.66761 / 3.33 ( 2625) link_NAG-ASN : bond 0.00041 / 0.02 ( 5) link_NAG-ASN : angle 1.46252 / 0.84 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.8343 (pp-130) cc_final: 0.7809 (ppp) REVERT: A 263 TRP cc_start: 0.7831 (m-10) cc_final: 0.7223 (m-10) REVERT: A 334 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: D 42 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8300 (mtp) REVERT: D 113 MET cc_start: 0.8591 (ppp) cc_final: 0.8068 (ppp) REVERT: D 221 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7489 (p90) REVERT: D 334 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6824 (mp10) REVERT: E 113 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8091 (ppp) REVERT: E 221 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7551 (p90) REVERT: B 187 MET cc_start: 0.9144 (mmm) cc_final: 0.8846 (mmm) REVERT: B 221 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7808 (p90) REVERT: C 178 MET cc_start: 0.9483 (ttm) cc_final: 0.9162 (ttp) REVERT: C 187 MET cc_start: 0.9068 (mmm) cc_final: 0.8641 (mmm) outliers start: 37 outliers final: 13 residues processed: 140 average time/residue: 0.4988 time to fit residues: 77.5054 Evaluate side-chains 131 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 334 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 136 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.090144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.066965 restraints weight = 34780.084| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.19 r_work: 0.2939 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15060 Z= 0.147 Angle : 0.609 12.108 20420 Z= 0.310 Chirality : 0.043 0.151 2300 Planarity : 0.003 0.031 2555 Dihedral : 4.758 23.296 1965 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.81 % Allowed : 14.52 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1785 helix: 2.72 (0.19), residues: 625 sheet: 0.77 (0.26), residues: 400 loop : -1.53 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.021 0.002 TYR B 433 PHE 0.033 0.002 PHE C 330 TRP 0.016 0.001 TRP E 267 HIS 0.002 0.001 HIS E 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (15050) covalent geometry : angle 0.60879 / 0.31 (20395) SS BOND : bond 0.00321 / 0.19 ( 5) SS BOND : angle 0.38236 / 0.19 ( 10) hydrogen bonds : bond 0.04092 / 2.74 ( 745) hydrogen bonds : angle 4.58143 / 3.27 ( 2625) link_NAG-ASN : bond 0.00164 / 0.10 ( 5) link_NAG-ASN : angle 1.11526 / 0.63 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8291 (pp-130) cc_final: 0.7947 (ppp) REVERT: A 334 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6889 (mp10) REVERT: D 32 MET cc_start: 0.6918 (tpp) cc_final: 0.6384 (tpp) REVERT: D 42 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8309 (mtp) REVERT: D 113 MET cc_start: 0.8609 (ppp) cc_final: 0.8053 (ppp) REVERT: D 221 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7653 (p90) REVERT: D 334 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6888 (mp10) REVERT: E 113 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8076 (ppp) REVERT: E 221 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7573 (p90) REVERT: B 187 MET cc_start: 0.9129 (mmm) cc_final: 0.8806 (mmm) REVERT: B 221 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7870 (p90) REVERT: C 178 MET cc_start: 0.9458 (ttm) cc_final: 0.9118 (ttp) REVERT: C 187 MET cc_start: 0.9088 (mmm) cc_final: 0.8664 (mmm) outliers start: 29 outliers final: 18 residues processed: 129 average time/residue: 0.4908 time to fit residues: 70.1132 Evaluate side-chains 136 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 334 GLN Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 428 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 51 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 176 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.090029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.066931 restraints weight = 34866.870| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.17 r_work: 0.2935 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15060 Z= 0.154 Angle : 0.617 11.302 20420 Z= 0.312 Chirality : 0.043 0.148 2300 Planarity : 0.003 0.031 2555 Dihedral : 4.738 25.387 1965 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.31 % Allowed : 14.02 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1785 helix: 2.71 (0.19), residues: 625 sheet: 0.65 (0.26), residues: 405 loop : -1.47 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.022 0.002 TYR B 433 PHE 0.027 0.002 PHE C 330 TRP 0.014 0.001 TRP C 263 HIS 0.002 0.001 HIS E 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (15050) covalent geometry : angle 0.61656 / 0.31 (20395) SS BOND : bond 0.00328 / 0.19 ( 5) SS BOND : angle 0.39899 / 0.20 ( 10) hydrogen bonds : bond 0.04065 / 2.72 ( 745) hydrogen bonds : angle 4.54753 / 3.25 ( 2625) link_NAG-ASN : bond 0.00112 / 0.07 ( 5) link_NAG-ASN : angle 1.19965 / 0.68 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8248 (pp-130) cc_final: 0.7936 (ppp) REVERT: A 334 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6845 (mp10) REVERT: D 32 MET cc_start: 0.7102 (tpp) cc_final: 0.6543 (tpp) REVERT: D 42 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8334 (mtp) REVERT: D 113 MET cc_start: 0.8605 (ppp) cc_final: 0.7891 (ppp) REVERT: D 221 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7657 (p90) REVERT: D 334 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: E 113 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8061 (ppp) REVERT: E 221 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7543 (p90) REVERT: B 187 MET cc_start: 0.9134 (mmm) cc_final: 0.8785 (mmm) REVERT: B 221 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7867 (p90) REVERT: C 178 MET cc_start: 0.9464 (ttm) cc_final: 0.9123 (ttp) REVERT: C 187 MET cc_start: 0.9087 (mmm) cc_final: 0.8632 (mmm) outliers start: 37 outliers final: 20 residues processed: 140 average time/residue: 0.4718 time to fit residues: 73.8681 Evaluate side-chains 138 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 334 GLN Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 428 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 38 optimal weight: 0.0170 chunk 112 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 10 optimal weight: 0.0270 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.091745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068868 restraints weight = 34521.202| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.18 r_work: 0.2977 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15060 Z= 0.115 Angle : 0.613 12.500 20420 Z= 0.304 Chirality : 0.042 0.151 2300 Planarity : 0.003 0.031 2555 Dihedral : 4.576 25.938 1965 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.56 % Allowed : 15.14 % Favored : 83.30 % 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: 0.88 (0.20), residues: 1785 helix: 2.71 (0.19), residues: 625 sheet: 0.74 (0.26), residues: 400 loop : -1.43 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 415 TYR 0.017 0.001 TYR E 433 PHE 0.024 0.001 PHE C 330 TRP 0.019 0.001 TRP C 263 HIS 0.002 0.000 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (15050) covalent geometry : angle 0.61320 / 0.30 (20395) SS BOND : bond 0.00283 / 0.17 ( 5) SS BOND : angle 0.20512 / 0.10 ( 10) hydrogen bonds : bond 0.03766 / 2.54 ( 745) hydrogen bonds : angle 4.38922 / 3.14 ( 2625) link_NAG-ASN : bond 0.00297 / 0.17 ( 5) link_NAG-ASN : angle 0.77199 / 0.43 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8976 (mppt) cc_final: 0.8636 (tppt) REVERT: A 263 TRP cc_start: 0.7738 (m-10) cc_final: 0.7195 (m-10) REVERT: A 334 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6797 (mp10) REVERT: D 32 MET cc_start: 0.7155 (tpp) cc_final: 0.6614 (tpp) REVERT: D 42 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8216 (mtp) REVERT: D 113 MET cc_start: 0.8617 (ppp) cc_final: 0.8134 (ppp) REVERT: D 221 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7614 (p90) REVERT: D 334 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: E 113 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8062 (ppp) REVERT: E 190 LEU cc_start: 0.8877 (tp) cc_final: 0.8364 (tp) REVERT: E 221 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7416 (p90) REVERT: B 187 MET cc_start: 0.9119 (mmm) cc_final: 0.8831 (mmm) REVERT: B 221 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7907 (p90) REVERT: C 105 ASP cc_start: 0.8808 (p0) cc_final: 0.8545 (p0) REVERT: C 113 MET cc_start: 0.8576 (ppp) cc_final: 0.8292 (pp-130) REVERT: C 178 MET cc_start: 0.9437 (ttm) cc_final: 0.9090 (ttp) REVERT: C 187 MET cc_start: 0.9076 (mmm) cc_final: 0.8613 (mmm) outliers start: 25 outliers final: 11 residues processed: 135 average time/residue: 0.5093 time to fit residues: 76.2920 Evaluate side-chains 133 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 334 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 428 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 99 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.090564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.067593 restraints weight = 34509.485| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.15 r_work: 0.2955 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15060 Z= 0.149 Angle : 0.632 13.759 20420 Z= 0.312 Chirality : 0.043 0.146 2300 Planarity : 0.003 0.031 2555 Dihedral : 4.594 25.284 1965 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.43 % Allowed : 15.70 % Favored : 82.87 % 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: 0.88 (0.20), residues: 1785 helix: 2.71 (0.19), residues: 625 sheet: 0.70 (0.26), residues: 400 loop : -1.39 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 415 TYR 0.020 0.002 TYR B 433 PHE 0.025 0.001 PHE C 330 TRP 0.019 0.001 TRP C 263 HIS 0.002 0.001 HIS E 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (15050) covalent geometry : angle 0.63154 / 0.31 (20395) SS BOND : bond 0.00315 / 0.19 ( 5) SS BOND : angle 0.36408 / 0.18 ( 10) hydrogen bonds : bond 0.03847 / 2.59 ( 745) hydrogen bonds : angle 4.41939 / 3.16 ( 2625) link_NAG-ASN : bond 0.00135 / 0.08 ( 5) link_NAG-ASN : angle 1.11367 / 0.63 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3710.02 seconds wall clock time: 64 minutes 8.82 seconds (3848.82 seconds total)