Starting phenix.real_space_refine on Fri Jun 13 06:25:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6n_23701/06_2025/7m6n_23701.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6n_23701/06_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_23701/06_2025/7m6n_23701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6n_23701/06_2025/7m6n_23701.map" model { file = "/net/cci-nas-00/data/ceres_data/7m6n_23701/06_2025/7m6n_23701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6n_23701/06_2025/7m6n_23701.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 1, 'ARG: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: {'PHE:plan': 1, 'ARG: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: {'PHE:plan': 1, 'ARG: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: {'PHE:plan': 1, 'ARG: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: {'PHE:plan': 1, 'ARG: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: 8.84, per 1000 atoms: 0.60 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: 3.36 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.78 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: 5.05 Time building geometry restraints manager: 4.03 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 34.600 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 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:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.003 TRP E 263 HIS 0.007 0.002 HIS B 239 PHE 0.052 0.006 PHE B 87 TYR 0.060 0.005 TYR A 433 ARG 0.012 0.002 ARG E 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 5) link_NAG-ASN : angle 2.85276 ( 15) hydrogen bonds : bond 0.16123 ( 745) hydrogen bonds : angle 6.97728 ( 2625) SS BOND : bond 0.00984 ( 5) SS BOND : angle 1.43996 ( 10) covalent geometry : bond 0.00867 (15050) covalent geometry : angle 1.27891 (20395) *********************** 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 : 1.645 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: 1.1992 time to fit residues: 284.9692 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 : 1.600 ------------------------------------------------------------------------------- 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 151 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 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 = 0.092947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070307 restraints weight = 34370.377| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.17 r_work: 0.3021 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1869 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= 0.157 Angle : 0.661 9.574 20420 Z= 0.352 Chirality : 0.045 0.177 2300 Planarity : 0.005 0.049 2555 Dihedral : 5.075 20.867 2076 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.25 % Allowed : 10.65 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1785 helix: 2.44 (0.19), residues: 660 sheet: 1.07 (0.27), residues: 380 loop : -1.38 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 263 HIS 0.002 0.000 HIS E 133 PHE 0.022 0.002 PHE C 87 TYR 0.026 0.002 TYR E 433 ARG 0.003 0.001 ARG E 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 5) link_NAG-ASN : angle 1.38116 ( 15) hydrogen bonds : bond 0.05260 ( 745) hydrogen bonds : angle 5.11069 ( 2625) SS BOND : bond 0.00466 ( 5) SS BOND : angle 0.52162 ( 10) covalent geometry : bond 0.00341 (15050) covalent geometry : angle 0.66026 (20395) *********************** 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 143 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8969 (mmm) cc_final: 0.8599 (mmm) REVERT: A 263 TRP cc_start: 0.8134 (m-10) cc_final: 0.7687 (m-10) REVERT: D 113 MET cc_start: 0.8569 (ppp) cc_final: 0.8245 (pp-130) REVERT: E 113 MET cc_start: 0.8561 (ppp) cc_final: 0.7997 (pp-130) REVERT: E 221 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7718 (p90) REVERT: B 187 MET cc_start: 0.8981 (mmm) cc_final: 0.8587 (mmm) REVERT: C 178 MET cc_start: 0.9388 (ttm) cc_final: 0.9100 (ttp) REVERT: C 187 MET cc_start: 0.8978 (mmm) cc_final: 0.8347 (mmm) outliers start: 20 outliers final: 4 residues processed: 137 average time/residue: 1.1469 time to fit residues: 174.9288 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 : 1.620 ------------------------------------------------------------------------------- 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.6622 > 50: distance: 53 - 71: 3.321 distance: 58 - 82: 3.246 distance: 62 - 90: 12.391 distance: 66 - 96: 7.413 distance: 71 - 72: 3.304 distance: 72 - 75: 6.930 distance: 73 - 82: 3.060 distance: 74 - 107: 7.411 distance: 75 - 76: 7.047 distance: 76 - 77: 5.342 distance: 76 - 78: 3.035 distance: 77 - 79: 4.061 distance: 78 - 80: 3.699 distance: 79 - 81: 5.809 distance: 82 - 83: 6.024 distance: 83 - 84: 3.506 distance: 83 - 86: 8.842 distance: 84 - 85: 5.239 distance: 84 - 90: 7.003 distance: 85 - 112: 10.619 distance: 86 - 87: 14.134 distance: 86 - 88: 16.083 distance: 87 - 89: 17.682 distance: 91 - 92: 3.636 distance: 91 - 94: 4.519 distance: 93 - 121: 9.090 distance: 94 - 95: 18.377 distance: 96 - 97: 5.411 distance: 97 - 100: 4.868 distance: 98 - 99: 4.765 distance: 98 - 107: 3.321 distance: 99 - 132: 17.289 distance: 101 - 102: 5.085 distance: 102 - 103: 7.125 distance: 103 - 104: 9.464 distance: 104 - 105: 18.681 distance: 104 - 106: 5.457 distance: 107 - 108: 4.244 distance: 108 - 109: 7.026 distance: 108 - 111: 9.002 distance: 109 - 110: 12.234 distance: 109 - 112: 4.450 distance: 110 - 140: 25.416 distance: 112 - 113: 5.511 distance: 113 - 116: 3.961 distance: 114 - 115: 4.871 distance: 114 - 121: 7.031 distance: 115 - 148: 16.735 distance: 116 - 117: 4.767 distance: 117 - 118: 12.102 distance: 118 - 119: 7.741 distance: 119 - 120: 7.387 distance: 121 - 122: 5.146 distance: 122 - 123: 10.135 distance: 122 - 125: 4.864 distance: 123 - 124: 7.550 distance: 123 - 132: 9.810 distance: 124 - 155: 4.334 distance: 125 - 126: 9.694 distance: 126 - 127: 9.864 distance: 127 - 128: 7.812 distance: 128 - 129: 8.027 distance: 129 - 130: 4.479 distance: 129 - 131: 7.135 distance: 132 - 133: 6.793 distance: 133 - 134: 9.712 distance: 133 - 136: 16.402 distance: 134 - 135: 24.902 distance: 134 - 140: 26.911 distance: 135 - 162: 25.109 distance: 136 - 137: 8.866 distance: 136 - 138: 24.023 distance: 137 - 139: 7.615 distance: 140 - 141: 31.303 distance: 141 - 142: 11.352 distance: 141 - 144: 21.463 distance: 142 - 143: 8.596 distance: 142 - 148: 11.166 distance: 143 - 168: 9.709 distance: 144 - 145: 11.650 distance: 145 - 146: 14.670 distance: 148 - 149: 5.428 distance: 149 - 152: 6.506 distance: 150 - 151: 5.804 distance: 151 - 179: 3.291 distance: 152 - 153: 8.341 distance: 152 - 154: 8.908