Starting phenix.real_space_refine on Fri Sep 27 02:37:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6n_23701/09_2024/7m6n_23701.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6n_23701/09_2024/7m6n_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6n_23701/09_2024/7m6n_23701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6n_23701/09_2024/7m6n_23701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6n_23701/09_2024/7m6n_23701.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6n_23701/09_2024/7m6n_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-5461/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: 7.78, per 1000 atoms: 0.53 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: 2.98 Conformation dependent library (CDL) restraints added in 1.6 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: 1.67 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: 4.71 Time building geometry restraints manager: 3.56 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.330 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.020 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:10.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.940 ------------------------------------------------------------------------------- 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 15050 Z= 0.566 Angle : 1.279 10.328 20395 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 215 time to evaluate : 1.569 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: 1.1777 time to fit residues: 279.5114 Evaluate side-chains 119 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15050 Z= 0.224 Angle : 0.660 9.574 20395 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 *********************** 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 fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 TRP cc_start: 0.8128 (m-10) cc_final: 0.7694 (m-10) REVERT: E 113 MET cc_start: 0.7972 (ppp) cc_final: 0.7571 (pp-130) REVERT: E 221 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.7153 (p90) REVERT: B 187 MET cc_start: 0.8607 (mmm) cc_final: 0.8372 (mmm) REVERT: C 178 MET cc_start: 0.8109 (ttm) cc_final: 0.7874 (ttp) REVERT: C 187 MET cc_start: 0.8550 (mmm) cc_final: 0.8250 (mmm) outliers start: 20 outliers final: 4 residues processed: 137 average time/residue: 1.1640 time to fit residues: 177.4802 Evaluate side-chains 108 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.664 ------------------------------------------------------------------------------- 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 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 145 optimal weight: 0.0050 chunk 162 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15050 Z= 0.197 Angle : 0.594 8.280 20395 Z= 0.312 Chirality : 0.043 0.159 2300 Planarity : 0.004 0.035 2555 Dihedral : 4.975 53.205 2072 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.81 % Allowed : 11.46 % Favored : 86.73 % 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: 0.96 (0.20), residues: 1785 helix: 2.60 (0.19), residues: 655 sheet: 1.05 (0.27), residues: 390 loop : -1.53 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 263 HIS 0.002 0.001 HIS E 133 PHE 0.037 0.002 PHE D 330 TYR 0.024 0.002 TYR B 433 ARG 0.005 0.000 ARG D 333 *********************** 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 142 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 TRP cc_start: 0.7953 (m-10) cc_final: 0.7582 (m-10) REVERT: D 221 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6954 (p90) REVERT: D 270 MET cc_start: 0.6010 (ppp) cc_final: 0.5681 (ppp) REVERT: E 113 MET cc_start: 0.8004 (ppp) cc_final: 0.7645 (ppp) REVERT: E 221 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.7047 (p90) REVERT: B 187 MET cc_start: 0.8552 (mmm) cc_final: 0.8350 (mmm) REVERT: B 221 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.6958 (p90) REVERT: C 178 MET cc_start: 0.8109 (ttm) cc_final: 0.7808 (ttp) outliers start: 29 outliers final: 3 residues processed: 126 average time/residue: 1.2423 time to fit residues: 173.2133 Evaluate side-chains 109 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 188 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** C 334 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15050 Z= 0.184 Angle : 0.565 8.091 20395 Z= 0.296 Chirality : 0.042 0.157 2300 Planarity : 0.003 0.041 2555 Dihedral : 4.698 20.989 2070 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.43 % Allowed : 12.02 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.20), residues: 1785 helix: 2.64 (0.19), residues: 655 sheet: 1.07 (0.27), residues: 390 loop : -1.53 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 267 HIS 0.002 0.001 HIS A 133 PHE 0.032 0.001 PHE A 330 TYR 0.021 0.002 TYR A 433 ARG 0.003 0.000 ARG C 242 *********************** 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 156 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 117 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 TRP cc_start: 0.7867 (m-10) cc_final: 0.7514 (m-10) REVERT: D 221 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6951 (p90) REVERT: E 113 MET cc_start: 0.8045 (ppp) cc_final: 0.7666 (ppp) REVERT: E 221 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.7010 (p90) REVERT: B 187 MET cc_start: 0.8565 (mmm) cc_final: 0.8359 (mmm) REVERT: B 221 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6895 (p90) REVERT: C 178 MET cc_start: 0.8159 (ttm) cc_final: 0.7866 (ttp) outliers start: 39 outliers final: 12 residues processed: 144 average time/residue: 1.0895 time to fit residues: 175.4505 Evaluate side-chains 123 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 80 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 188 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 0.0270 chunk 129 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 15050 Z= 0.417 Angle : 0.669 8.201 20395 Z= 0.352 Chirality : 0.046 0.149 2300 Planarity : 0.004 0.039 2555 Dihedral : 5.160 23.645 2070 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.68 % Allowed : 11.84 % Favored : 85.48 % 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: 0.82 (0.20), residues: 1785 helix: 2.49 (0.19), residues: 660 sheet: 0.73 (0.26), residues: 405 loop : -1.52 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 267 HIS 0.006 0.001 HIS A 133 PHE 0.039 0.003 PHE E 330 TYR 0.031 0.002 TYR B 433 ARG 0.006 0.001 ARG C 242 *********************** 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 153 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 110 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8149 (pp-130) cc_final: 0.7875 (ppp) REVERT: E 113 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7603 (ppp) REVERT: B 221 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.6983 (p90) REVERT: C 113 MET cc_start: 0.8049 (ppp) cc_final: 0.7785 (pp-130) REVERT: C 178 MET cc_start: 0.8183 (ttm) cc_final: 0.7907 (ttp) outliers start: 43 outliers final: 25 residues processed: 137 average time/residue: 1.2194 time to fit residues: 185.9148 Evaluate side-chains 131 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 265 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL 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 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 416 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 188 ASN 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 58 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 174 optimal weight: 0.0770 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 0.0030 overall best weight: 0.4348 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15050 Z= 0.164 Angle : 0.579 8.629 20395 Z= 0.300 Chirality : 0.043 0.162 2300 Planarity : 0.003 0.032 2555 Dihedral : 4.842 22.341 2070 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.12 % Allowed : 12.96 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.81 (0.20), residues: 1785 helix: 2.76 (0.19), residues: 625 sheet: 0.74 (0.26), residues: 405 loop : -1.61 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 263 HIS 0.002 0.000 HIS E 225 PHE 0.026 0.001 PHE E 330 TYR 0.021 0.002 TYR A 433 ARG 0.002 0.000 ARG C 83 *********************** 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 149 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 TRP cc_start: 0.7886 (m-10) cc_final: 0.7439 (m-10) REVERT: D 32 MET cc_start: 0.6954 (tpp) cc_final: 0.6064 (tpp) REVERT: D 221 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6874 (p90) REVERT: E 113 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7729 (ppp) REVERT: E 221 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.6963 (p90) REVERT: B 221 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.7114 (p90) REVERT: C 178 MET cc_start: 0.8148 (ttm) cc_final: 0.7877 (ttp) outliers start: 34 outliers final: 14 residues processed: 132 average time/residue: 1.2120 time to fit residues: 177.6922 Evaluate side-chains 124 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 221 TYR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 221 TYR 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 427 ILE Chi-restraints excluded: chain C residue 188 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15050 Z= 0.202 Angle : 0.598 10.213 20395 Z= 0.304 Chirality : 0.043 0.155 2300 Planarity : 0.003 0.031 2555 Dihedral : 4.753 22.712 2070 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.43 % Allowed : 13.33 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.81 (0.20), residues: 1785 helix: 2.74 (0.19), residues: 625 sheet: 0.69 (0.26), residues: 405 loop : -1.57 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 267 HIS 0.002 0.001 HIS A 133 PHE 0.021 0.001 PHE E 330 TYR 0.020 0.002 TYR B 433 ARG 0.003 0.000 ARG C 242 *********************** 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 150 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 111 time to evaluate : 1.748 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.7866 (m-10) cc_final: 0.7414 (m-10) REVERT: D 221 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6889 (p90) REVERT: E 113 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7745 (ppp) REVERT: E 221 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6953 (p90) REVERT: B 221 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.7159 (p90) REVERT: C 178 MET cc_start: 0.8179 (ttm) cc_final: 0.7883 (ttp) outliers start: 39 outliers final: 14 residues processed: 136 average time/residue: 1.1799 time to fit residues: 178.5511 Evaluate side-chains 129 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.737 ------------------------------------------------------------------------------- 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 221 TYR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 221 TYR 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 C residue 78 THR Chi-restraints excluded: chain C residue 188 ASN 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 107 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 118 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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** C 334 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15050 Z= 0.176 Angle : 0.600 12.546 20395 Z= 0.300 Chirality : 0.042 0.154 2300 Planarity : 0.003 0.030 2555 Dihedral : 4.626 22.698 2070 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.87 % Allowed : 14.52 % Favored : 83.61 % 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: 0.84 (0.20), residues: 1785 helix: 2.75 (0.19), residues: 625 sheet: 0.67 (0.26), residues: 405 loop : -1.51 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 263 HIS 0.002 0.000 HIS E 225 PHE 0.022 0.001 PHE C 330 TYR 0.018 0.001 TYR B 433 ARG 0.002 0.000 ARG C 242 *********************** 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 146 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.715 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.7753 (m-10) cc_final: 0.7326 (m-10) REVERT: D 32 MET cc_start: 0.6565 (tpp) cc_final: 0.5466 (tpp) REVERT: D 221 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6851 (p90) REVERT: E 113 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7742 (ppp) REVERT: E 221 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.6946 (p90) REVERT: B 221 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.7153 (p90) REVERT: C 113 MET cc_start: 0.8194 (ppp) cc_final: 0.7822 (pp-130) outliers start: 30 outliers final: 16 residues processed: 134 average time/residue: 1.1583 time to fit residues: 173.2892 Evaluate side-chains 133 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.585 ------------------------------------------------------------------------------- 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 221 TYR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 181 GLU 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 171 MET Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 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 428 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 0.0060 chunk 146 optimal weight: 3.9990 chunk 152 optimal weight: 0.3980 chunk 106 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15050 Z= 0.168 Angle : 0.607 13.093 20395 Z= 0.300 Chirality : 0.042 0.153 2300 Planarity : 0.003 0.030 2555 Dihedral : 4.542 22.850 2070 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.99 % Allowed : 14.70 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.85 (0.20), residues: 1785 helix: 2.74 (0.19), residues: 625 sheet: 0.65 (0.26), residues: 405 loop : -1.47 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 263 HIS 0.002 0.000 HIS E 225 PHE 0.024 0.001 PHE B 330 TYR 0.017 0.001 TYR B 433 ARG 0.002 0.000 ARG C 333 *********************** 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 148 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 1.981 Fit side-chains REVERT: A 263 TRP cc_start: 0.7717 (m-10) cc_final: 0.7380 (m-10) REVERT: D 32 MET cc_start: 0.6680 (tpp) cc_final: 0.5565 (tpp) REVERT: D 221 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6836 (p90) REVERT: D 263 TRP cc_start: 0.7819 (m-10) cc_final: 0.7429 (m-10) REVERT: E 113 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7733 (ppp) REVERT: E 221 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6798 (p90) REVERT: B 221 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.7122 (p90) REVERT: C 113 MET cc_start: 0.8174 (ppp) cc_final: 0.7691 (pp-130) outliers start: 32 outliers final: 15 residues processed: 135 average time/residue: 1.1698 time to fit residues: 175.5893 Evaluate side-chains 131 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 221 TYR 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 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 431 ILE 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 78 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 428 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15050 Z= 0.229 Angle : 0.638 12.938 20395 Z= 0.314 Chirality : 0.043 0.151 2300 Planarity : 0.003 0.031 2555 Dihedral : 4.611 23.531 2070 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.31 % Allowed : 15.20 % 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 (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: 0.86 (0.20), residues: 1785 helix: 2.75 (0.19), residues: 625 sheet: 0.62 (0.26), residues: 405 loop : -1.43 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 263 HIS 0.003 0.001 HIS A 133 PHE 0.023 0.001 PHE B 330 TYR 0.020 0.002 TYR B 433 ARG 0.003 0.000 ARG C 242 ********************** 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 132 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.697 Fit side-chains REVERT: A 263 TRP cc_start: 0.7785 (m-10) cc_final: 0.7335 (m-10) REVERT: D 32 MET cc_start: 0.6800 (tpp) cc_final: 0.5744 (tpp) REVERT: D 113 MET cc_start: 0.8194 (ppp) cc_final: 0.7980 (pp-130) REVERT: D 221 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6879 (p90) REVERT: D 263 TRP cc_start: 0.7860 (m-10) cc_final: 0.7434 (m-10) REVERT: E 113 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7729 (ppp) REVERT: E 221 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.6851 (p90) REVERT: B 221 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.7169 (p90) outliers start: 21 outliers final: 14 residues processed: 123 average time/residue: 1.2489 time to fit residues: 170.0740 Evaluate side-chains 129 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.664 ------------------------------------------------------------------------------- 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 221 TYR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 428 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9990 chunk 43 optimal weight: 0.0170 chunk 131 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 146 optimal weight: 0.0570 chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.092580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.069794 restraints weight = 34335.145| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.17 r_work: 0.3006 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15050 Z= 0.160 Angle : 0.621 13.248 20395 Z= 0.303 Chirality : 0.042 0.155 2300 Planarity : 0.003 0.030 2555 Dihedral : 4.487 25.235 2070 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.43 % Allowed : 15.08 % 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 (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: 0.88 (0.20), residues: 1785 helix: 2.73 (0.19), residues: 625 sheet: 0.70 (0.26), residues: 400 loop : -1.41 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 263 HIS 0.002 0.000 HIS D 335 PHE 0.023 0.001 PHE B 330 TYR 0.015 0.001 TYR B 433 ARG 0.006 0.000 ARG D 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4081.79 seconds wall clock time: 72 minutes 50.04 seconds (4370.04 seconds total)