Starting phenix.real_space_refine on Sat Aug 23 21:16:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6n_23701/08_2025/7m6n_23701.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6n_23701/08_2025/7m6n_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m6n_23701/08_2025/7m6n_23701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6n_23701/08_2025/7m6n_23701.map" model { file = "/net/cci-nas-00/data/ceres_data/7m6n_23701/08_2025/7m6n_23701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6n_23701/08_2025/7m6n_23701.cif" } 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-2.0-5787/lib/python3.9/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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.61, per 1000 atoms: 0.25 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: 1.31 Conformation dependent library (CDL) restraints added in 668.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.51 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: 2.85 Time building geometry restraints manager: 1.74 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: 8428 16.67 - 33.34: 513 33.34 - 50.02: 114 50.02 - 66.69: 20 66.69 - 83.36: 5 Dihedral angle restraints: 9080 sinusoidal: 3740 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 9077 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.190 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:7.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 : 11.868 83.360 5595 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 aren 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 covalent geometry : bond 0.00867 (15050) covalent geometry : angle 1.27891 (20395) SS BOND : bond 0.00984 ( 5) SS BOND : angle 1.43996 ( 10) hydrogen bonds : bond 0.16123 ( 745) hydrogen bonds : angle 6.97728 ( 2625) link_NAG-ASN : bond 0.00541 ( 5) link_NAG-ASN : angle 2.85276 ( 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 : 0.553 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: 0.7636 (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: 0.6300 time to fit residues: 148.8534 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 : 0.740 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.092950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.070092 restraints weight = 34500.708| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.19 r_work: 0.3026 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1852 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 : 0.667 9.526 20420 Z= 0.355 Chirality : 0.045 0.179 2300 Planarity : 0.005 0.049 2555 Dihedral : 5.063 20.941 2076 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.12 % Allowed : 10.72 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.20), residues: 1785 helix: 2.45 (0.19), residues: 660 sheet: 1.07 (0.27), residues: 380 loop : -1.39 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 242 TYR 0.025 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 covalent geometry : bond 0.00349 (15050) covalent geometry : angle 0.66659 (20395) SS BOND : bond 0.00486 ( 5) SS BOND : angle 0.55027 ( 10) hydrogen bonds : bond 0.05327 ( 745) hydrogen bonds : angle 5.11768 ( 2625) link_NAG-ASN : bond 0.00296 ( 5) link_NAG-ASN : angle 1.38603 ( 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 : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8962 (mmm) cc_final: 0.8595 (mmm) REVERT: A 263 TRP cc_start: 0.8135 (m-10) cc_final: 0.7685 (m-10) REVERT: D 113 MET cc_start: 0.8561 (ppp) cc_final: 0.8268 (pp-130) REVERT: E 113 MET cc_start: 0.8574 (ppp) cc_final: 0.7997 (pp-130) REVERT: E 221 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7715 (p90) REVERT: B 187 MET cc_start: 0.8979 (mmm) cc_final: 0.8582 (mmm) REVERT: C 178 MET cc_start: 0.9397 (ttm) cc_final: 0.9112 (ttp) REVERT: C 187 MET cc_start: 0.8972 (mmm) cc_final: 0.8335 (mmm) outliers start: 18 outliers final: 4 residues processed: 135 average time/residue: 0.6007 time to fit residues: 90.1970 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 : 0.641 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3538 r_free = 0.3538 target = 0.090756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.068014 restraints weight = 34904.467| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.19 r_work: 0.2964 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15060 Z= 0.181 Angle : 0.624 8.250 20420 Z= 0.329 Chirality : 0.044 0.161 2300 Planarity : 0.004 0.037 2555 Dihedral : 5.179 58.920 2072 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.87 % Allowed : 11.59 % Favored : 86.54 % 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 aren not related in a simple way. whole: 0.96 (0.20), residues: 1785 helix: 2.62 (0.19), residues: 655 sheet: 1.04 (0.27), residues: 390 loop : -1.55 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.026 0.002 TYR B 433 PHE 0.036 0.002 PHE D 330 TRP 0.008 0.001 TRP E 267 HIS 0.003 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00419 (15050) covalent geometry : angle 0.62266 (20395) SS BOND : bond 0.00421 ( 5) SS BOND : angle 0.52712 ( 10) hydrogen bonds : bond 0.04814 ( 745) hydrogen bonds : angle 4.92338 ( 2625) link_NAG-ASN : bond 0.00108 ( 5) link_NAG-ASN : angle 1.53178 ( 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 139 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9042 (mmm) cc_final: 0.8658 (mmm) REVERT: A 263 TRP cc_start: 0.7995 (m-10) cc_final: 0.7567 (m-10) REVERT: D 113 MET cc_start: 0.8564 (ppp) cc_final: 0.8188 (pp-130) REVERT: D 221 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7696 (p90) REVERT: D 270 MET cc_start: 0.6230 (ppp) cc_final: 0.5765 (ppp) REVERT: E 113 MET cc_start: 0.8566 (ppp) cc_final: 0.8008 (ppp) REVERT: E 221 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7709 (p90) REVERT: B 187 MET cc_start: 0.9047 (mmm) cc_final: 0.8706 (mmm) REVERT: B 221 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7668 (p90) REVERT: C 178 MET cc_start: 0.9424 (ttm) cc_final: 0.9117 (ttp) REVERT: C 187 MET cc_start: 0.8976 (mmm) cc_final: 0.8421 (mmm) outliers start: 30 outliers final: 3 residues processed: 124 average time/residue: 0.6593 time to fit residues: 90.0581 Evaluate side-chains 107 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.0770 chunk 47 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3560 r_free = 0.3560 target = 0.091967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069361 restraints weight = 34566.432| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.18 r_work: 0.2991 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15060 Z= 0.126 Angle : 0.566 8.146 20420 Z= 0.297 Chirality : 0.042 0.159 2300 Planarity : 0.003 0.034 2555 Dihedral : 4.806 21.280 2070 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.37 % Allowed : 11.84 % Favored : 85.79 % 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 aren not related in a simple way. whole: 0.97 (0.20), residues: 1785 helix: 2.62 (0.19), residues: 655 sheet: 1.07 (0.27), residues: 390 loop : -1.54 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 333 TYR 0.022 0.002 TYR A 433 PHE 0.031 0.001 PHE C 330 TRP 0.012 0.001 TRP C 263 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00277 (15050) covalent geometry : angle 0.56552 (20395) SS BOND : bond 0.00300 ( 5) SS BOND : angle 0.24552 ( 10) hydrogen bonds : bond 0.04246 ( 745) hydrogen bonds : angle 4.71068 ( 2625) link_NAG-ASN : bond 0.00271 ( 5) link_NAG-ASN : angle 1.04859 ( 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 149 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9064 (mmm) cc_final: 0.8614 (mmm) REVERT: A 263 TRP cc_start: 0.7946 (m-10) cc_final: 0.7545 (m-10) REVERT: D 113 MET cc_start: 0.8606 (ppp) cc_final: 0.8278 (pp-130) REVERT: D 221 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7678 (p90) REVERT: D 270 MET cc_start: 0.6121 (ppp) cc_final: 0.5771 (ppp) REVERT: E 113 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8113 (ppp) REVERT: E 221 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7619 (p90) REVERT: E 263 TRP cc_start: 0.7753 (m-10) cc_final: 0.7479 (m-10) REVERT: B 187 MET cc_start: 0.9060 (mmm) cc_final: 0.8647 (mmm) REVERT: B 221 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7644 (p90) REVERT: C 178 MET cc_start: 0.9427 (ttm) cc_final: 0.9116 (ttp) REVERT: C 187 MET cc_start: 0.9059 (mmm) cc_final: 0.8397 (mmm) outliers start: 38 outliers final: 10 residues processed: 137 average time/residue: 0.5924 time to fit residues: 90.1147 Evaluate side-chains 116 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 221 TYR 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 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: 0.7980 chunk 30 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.091548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068573 restraints weight = 34714.649| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.19 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: 0.8294 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15060 Z= 0.133 Angle : 0.569 8.707 20420 Z= 0.296 Chirality : 0.042 0.155 2300 Planarity : 0.003 0.034 2555 Dihedral : 4.711 22.118 2070 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.06 % Allowed : 12.02 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.20), residues: 1785 helix: 2.77 (0.19), residues: 625 sheet: 0.97 (0.26), residues: 390 loop : -1.63 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.021 0.002 TYR A 433 PHE 0.036 0.001 PHE E 330 TRP 0.024 0.001 TRP A 267 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00301 (15050) covalent geometry : angle 0.56881 (20395) SS BOND : bond 0.00297 ( 5) SS BOND : angle 0.27629 ( 10) hydrogen bonds : bond 0.04107 ( 745) hydrogen bonds : angle 4.64046 ( 2625) link_NAG-ASN : bond 0.00202 ( 5) link_NAG-ASN : angle 1.09076 ( 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 140 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8493 (pp-130) cc_final: 0.7929 (ppp) REVERT: A 187 MET cc_start: 0.9096 (mmm) cc_final: 0.8851 (mmm) REVERT: A 263 TRP cc_start: 0.7833 (m-10) cc_final: 0.7422 (m-10) REVERT: D 113 MET cc_start: 0.8602 (ppp) cc_final: 0.8085 (ppp) REVERT: D 221 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7572 (p90) REVERT: D 270 MET cc_start: 0.5974 (ppp) cc_final: 0.5637 (ppp) REVERT: E 113 MET cc_start: 0.8642 (ppp) cc_final: 0.8004 (ppp) REVERT: E 221 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7625 (p90) REVERT: B 187 MET cc_start: 0.9098 (mmm) cc_final: 0.8629 (mmm) REVERT: B 221 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7647 (p90) REVERT: C 178 MET cc_start: 0.9426 (ttm) cc_final: 0.9089 (ttp) REVERT: C 187 MET cc_start: 0.9065 (mmm) cc_final: 0.8537 (mmm) outliers start: 33 outliers final: 13 residues processed: 128 average time/residue: 0.6104 time to fit residues: 86.6312 Evaluate side-chains 122 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 320 SER 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 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 320 SER Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 3 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 161 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3528 r_free = 0.3528 target = 0.090310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.067323 restraints weight = 34696.490| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.19 r_work: 0.2947 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15060 Z= 0.166 Angle : 0.585 9.045 20420 Z= 0.305 Chirality : 0.043 0.151 2300 Planarity : 0.003 0.032 2555 Dihedral : 4.775 23.118 2070 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.18 % Allowed : 12.71 % Favored : 85.11 % 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 aren not related in a simple way. whole: 0.84 (0.20), residues: 1785 helix: 2.77 (0.19), residues: 625 sheet: 0.80 (0.26), residues: 405 loop : -1.62 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.023 0.002 TYR A 433 PHE 0.027 0.002 PHE E 330 TRP 0.009 0.001 TRP A 267 HIS 0.005 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00385 (15050) covalent geometry : angle 0.58431 (20395) SS BOND : bond 0.00334 ( 5) SS BOND : angle 0.45739 ( 10) hydrogen bonds : bond 0.04186 ( 745) hydrogen bonds : angle 4.66641 ( 2625) link_NAG-ASN : bond 0.00105 ( 5) link_NAG-ASN : angle 1.32150 ( 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: 35 poor density : 112 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8435 (pp-130) cc_final: 0.7903 (ppp) REVERT: A 263 TRP cc_start: 0.7856 (m-10) cc_final: 0.7273 (m-10) REVERT: D 42 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8152 (mtp) REVERT: D 113 MET cc_start: 0.8599 (ppp) cc_final: 0.8091 (ppp) REVERT: D 221 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7642 (p90) REVERT: D 270 MET cc_start: 0.6001 (ppp) cc_final: 0.5692 (ppp) REVERT: D 334 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6869 (mp10) REVERT: E 113 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8120 (ppp) REVERT: E 221 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.7609 (p90) REVERT: B 187 MET cc_start: 0.9126 (mmm) cc_final: 0.8818 (mmm) REVERT: B 221 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7740 (p90) REVERT: C 178 MET cc_start: 0.9447 (ttm) cc_final: 0.9111 (ttp) REVERT: C 187 MET cc_start: 0.9079 (mmm) cc_final: 0.8593 (mmm) outliers start: 35 outliers final: 13 residues processed: 134 average time/residue: 0.5984 time to fit residues: 89.0917 Evaluate side-chains 123 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain D residue 42 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 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 115 ASP 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 221 TYR Chi-restraints excluded: chain C residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 145 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 163 optimal weight: 0.2980 chunk 112 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3533 r_free = 0.3533 target = 0.090724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.067725 restraints weight = 34611.746| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.20 r_work: 0.2950 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15060 Z= 0.141 Angle : 0.581 8.714 20420 Z= 0.300 Chirality : 0.043 0.154 2300 Planarity : 0.003 0.031 2555 Dihedral : 4.732 22.977 2070 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.55 % Allowed : 12.96 % Favored : 84.49 % 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 aren not related in a simple way. whole: 0.82 (0.20), residues: 1785 helix: 2.76 (0.19), residues: 625 sheet: 0.75 (0.26), residues: 405 loop : -1.61 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 415 TYR 0.021 0.002 TYR A 433 PHE 0.022 0.001 PHE E 330 TRP 0.020 0.001 TRP A 267 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00323 (15050) covalent geometry : angle 0.58070 (20395) SS BOND : bond 0.00306 ( 5) SS BOND : angle 0.34376 ( 10) hydrogen bonds : bond 0.04065 ( 745) hydrogen bonds : angle 4.59249 ( 2625) link_NAG-ASN : bond 0.00183 ( 5) link_NAG-ASN : angle 1.10160 ( 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 148 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8348 (pp-130) cc_final: 0.7836 (ppp) REVERT: D 42 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8126 (mtp) REVERT: D 113 MET cc_start: 0.8602 (ppp) cc_final: 0.8079 (ppp) REVERT: D 221 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7697 (p90) REVERT: D 270 MET cc_start: 0.5937 (ppp) cc_final: 0.5712 (ppp) REVERT: D 334 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6867 (mp10) REVERT: E 113 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8097 (ppp) REVERT: E 221 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7607 (p90) REVERT: B 187 MET cc_start: 0.9121 (mmm) cc_final: 0.8791 (mmm) REVERT: B 221 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7853 (p90) REVERT: C 178 MET cc_start: 0.9448 (ttm) cc_final: 0.9113 (ttp) REVERT: C 187 MET cc_start: 0.9077 (mmm) cc_final: 0.8549 (mmm) outliers start: 41 outliers final: 21 residues processed: 134 average time/residue: 0.6213 time to fit residues: 92.1562 Evaluate side-chains 133 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 A residue 431 ILE Chi-restraints excluded: chain D residue 42 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 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 181 GLU 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 115 ASP 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 115 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 136 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3541 r_free = 0.3541 target = 0.091071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.068108 restraints weight = 34612.116| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.18 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: 0.8305 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15060 Z= 0.125 Angle : 0.578 9.851 20420 Z= 0.295 Chirality : 0.042 0.154 2300 Planarity : 0.003 0.031 2555 Dihedral : 4.655 22.885 2070 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.37 % Allowed : 13.64 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.20), residues: 1785 helix: 3.14 (0.19), residues: 595 sheet: 0.74 (0.26), residues: 405 loop : -1.35 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 242 TYR 0.019 0.002 TYR B 433 PHE 0.019 0.001 PHE C 330 TRP 0.013 0.001 TRP C 263 HIS 0.002 0.000 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00283 (15050) covalent geometry : angle 0.57745 (20395) SS BOND : bond 0.00289 ( 5) SS BOND : angle 0.25555 ( 10) hydrogen bonds : bond 0.03929 ( 745) hydrogen bonds : angle 4.51494 ( 2625) link_NAG-ASN : bond 0.00211 ( 5) link_NAG-ASN : angle 1.00168 ( 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 149 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8320 (pp-130) cc_final: 0.7811 (ppp) REVERT: A 263 TRP cc_start: 0.7762 (m-10) cc_final: 0.7179 (m-10) REVERT: D 32 MET cc_start: 0.6858 (tpp) cc_final: 0.6318 (tpp) REVERT: D 42 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8229 (mtp) REVERT: D 113 MET cc_start: 0.8594 (ppp) cc_final: 0.8019 (ppp) REVERT: D 221 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7656 (p90) REVERT: D 270 MET cc_start: 0.5886 (ppp) cc_final: 0.5543 (ppp) REVERT: D 334 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6932 (mp10) REVERT: E 113 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8071 (ppp) REVERT: E 221 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7540 (p90) REVERT: B 187 MET cc_start: 0.9125 (mmm) cc_final: 0.8767 (mmm) REVERT: B 221 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7898 (p90) REVERT: C 178 MET cc_start: 0.9446 (ttm) cc_final: 0.9094 (ttp) REVERT: C 187 MET cc_start: 0.9076 (mmm) cc_final: 0.8618 (mmm) outliers start: 38 outliers final: 22 residues processed: 137 average time/residue: 0.6008 time to fit residues: 91.5704 Evaluate side-chains 137 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain D residue 42 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 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 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 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=1.50 ------------------------------------------------------------------------------- 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: 0.1980 chunk 118 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3542 r_free = 0.3542 target = 0.091271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.068375 restraints weight = 34809.458| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.18 r_work: 0.2964 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2982 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= 0.128 Angle : 0.591 11.012 20420 Z= 0.298 Chirality : 0.042 0.154 2300 Planarity : 0.003 0.030 2555 Dihedral : 4.605 22.733 2070 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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 aren not related in a simple way. whole: 1.07 (0.20), residues: 1785 helix: 3.14 (0.19), residues: 595 sheet: 0.71 (0.26), residues: 405 loop : -1.31 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.019 0.002 TYR B 433 PHE 0.025 0.001 PHE B 330 TRP 0.015 0.001 TRP E 267 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00293 (15050) covalent geometry : angle 0.59034 (20395) SS BOND : bond 0.00290 ( 5) SS BOND : angle 0.26572 ( 10) hydrogen bonds : bond 0.03864 ( 745) hydrogen bonds : angle 4.47450 ( 2625) link_NAG-ASN : bond 0.00195 ( 5) link_NAG-ASN : angle 1.04040 ( 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 151 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.8264 (pp-130) cc_final: 0.7882 (ppp) REVERT: A 263 TRP cc_start: 0.7741 (m-10) cc_final: 0.7319 (m-10) REVERT: D 32 MET cc_start: 0.6986 (tpp) cc_final: 0.6428 (tpp) REVERT: D 42 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8265 (mtp) REVERT: D 113 MET cc_start: 0.8601 (ppp) cc_final: 0.8055 (ppp) REVERT: D 221 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7651 (p90) REVERT: D 270 MET cc_start: 0.5905 (ppp) cc_final: 0.5651 (ppp) REVERT: D 334 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6900 (mp10) REVERT: E 113 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8076 (ppp) REVERT: E 221 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7528 (p90) REVERT: E 334 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6682 (mp10) REVERT: B 187 MET cc_start: 0.9129 (mmm) cc_final: 0.8764 (mmm) REVERT: B 221 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7895 (p90) REVERT: B 270 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6133 (tmm) REVERT: C 178 MET cc_start: 0.9455 (ttm) cc_final: 0.9100 (ttp) REVERT: C 187 MET cc_start: 0.9088 (mmm) cc_final: 0.8608 (mmm) outliers start: 37 outliers final: 22 residues processed: 138 average time/residue: 0.6170 time to fit residues: 94.3798 Evaluate side-chains 139 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 320 SER 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 221 TYR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 334 GLN 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 270 MET 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: 1.9990 chunk 106 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 110 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.068299 restraints weight = 34580.868| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.19 r_work: 0.2966 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15060 Z= 0.129 Angle : 0.597 12.253 20420 Z= 0.300 Chirality : 0.042 0.153 2300 Planarity : 0.003 0.031 2555 Dihedral : 4.596 22.683 2070 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.99 % Allowed : 14.27 % Favored : 83.74 % 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 aren not related in a simple way. whole: 1.08 (0.20), residues: 1785 helix: 3.12 (0.19), residues: 595 sheet: 0.69 (0.26), residues: 405 loop : -1.27 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.019 0.002 TYR B 433 PHE 0.026 0.001 PHE A 330 TRP 0.016 0.001 TRP C 263 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00297 (15050) covalent geometry : angle 0.59699 (20395) SS BOND : bond 0.00289 ( 5) SS BOND : angle 0.26877 ( 10) hydrogen bonds : bond 0.03825 ( 745) hydrogen bonds : angle 4.45330 ( 2625) link_NAG-ASN : bond 0.00196 ( 5) link_NAG-ASN : angle 1.02964 ( 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 143 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.8215 (pp-130) cc_final: 0.7840 (ppp) REVERT: A 263 TRP cc_start: 0.7735 (m-10) cc_final: 0.7311 (m-10) REVERT: D 32 MET cc_start: 0.7001 (tpp) cc_final: 0.6449 (tpp) REVERT: D 42 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8346 (mtp) REVERT: D 113 MET cc_start: 0.8567 (ppp) cc_final: 0.7800 (ppp) REVERT: D 221 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7665 (p90) REVERT: D 270 MET cc_start: 0.5900 (ppp) cc_final: 0.5645 (ppp) REVERT: E 113 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8089 (ppp) REVERT: E 221 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7519 (p90) REVERT: B 187 MET cc_start: 0.9136 (mmm) cc_final: 0.8759 (mmm) REVERT: B 221 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7856 (p90) REVERT: B 270 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6129 (tmm) REVERT: C 178 MET cc_start: 0.9451 (ttm) cc_final: 0.9087 (ttp) REVERT: C 187 MET cc_start: 0.9088 (mmm) cc_final: 0.8595 (mmm) outliers start: 32 outliers final: 22 residues processed: 132 average time/residue: 0.6049 time to fit residues: 88.4327 Evaluate side-chains 137 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 78 THR 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 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 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 270 MET 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 99 optimal weight: 0.4980 chunk 146 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3517 r_free = 0.3517 target = 0.089735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.066573 restraints weight = 34578.270| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.18 r_work: 0.2937 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15060 Z= 0.176 Angle : 0.621 11.913 20420 Z= 0.316 Chirality : 0.043 0.150 2300 Planarity : 0.003 0.031 2555 Dihedral : 4.719 23.558 2070 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.81 % Allowed : 14.70 % Favored : 83.49 % 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 aren not related in a simple way. whole: 1.07 (0.20), residues: 1785 helix: 3.10 (0.19), residues: 595 sheet: 0.65 (0.26), residues: 405 loop : -1.24 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 242 TYR 0.023 0.002 TYR B 433 PHE 0.024 0.002 PHE B 330 TRP 0.017 0.001 TRP C 263 HIS 0.004 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00414 (15050) covalent geometry : angle 0.62056 (20395) SS BOND : bond 0.00334 ( 5) SS BOND : angle 0.48126 ( 10) hydrogen bonds : bond 0.04045 ( 745) hydrogen bonds : angle 4.53390 ( 2625) link_NAG-ASN : bond 0.00088 ( 5) link_NAG-ASN : angle 1.36328 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4436.54 seconds wall clock time: 76 minutes 58.06 seconds (4618.06 seconds total)