Starting phenix.real_space_refine on Fri May 16 18:38:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6n_23701/05_2025/7m6n_23701.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6n_23701/05_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_23701/05_2025/7m6n_23701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6n_23701/05_2025/7m6n_23701.map" model { file = "/net/cci-nas-00/data/ceres_data/7m6n_23701/05_2025/7m6n_23701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6n_23701/05_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-5687/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: 9.02, per 1000 atoms: 0.61 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: 3.39 Conformation dependent library (CDL) restraints added in 1.8 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: 1.96 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: 5.25 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: 1.880 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.830 Find NCS groups from input model: 0.290 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: 0.010 Load rotamer database and sin/cos tables:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.500 ------------------------------------------------------------------------------- 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 : 1.620 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: 1.2095 time to fit residues: 287.2209 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 : 1.738 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070309 restraints weight = 34370.162| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.16 r_work: 0.3021 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 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 1.38113 ( 15) hydrogen bonds : bond 0.05260 ( 745) hydrogen bonds : angle 5.11072 ( 2625) SS BOND : bond 0.00466 ( 5) SS BOND : angle 0.52163 ( 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 : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8970 (mmm) cc_final: 0.8600 (mmm) REVERT: A 263 TRP cc_start: 0.8134 (m-10) cc_final: 0.7687 (m-10) REVERT: D 113 MET cc_start: 0.8568 (ppp) cc_final: 0.8244 (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: 0.7717 (p90) REVERT: B 187 MET cc_start: 0.8981 (mmm) cc_final: 0.8587 (mmm) REVERT: C 178 MET cc_start: 0.9386 (ttm) cc_final: 0.9099 (ttp) REVERT: C 187 MET cc_start: 0.8979 (mmm) cc_final: 0.8348 (mmm) outliers start: 20 outliers final: 4 residues processed: 137 average time/residue: 1.1201 time to fit residues: 171.2228 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 : 1.651 ------------------------------------------------------------------------------- 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 137 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 0.0670 overall best weight: 0.6522 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.093086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070518 restraints weight = 34294.574| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.21 r_work: 0.3021 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15060 Z= 0.131 Angle : 0.587 8.408 20420 Z= 0.309 Chirality : 0.043 0.161 2300 Planarity : 0.004 0.035 2555 Dihedral : 4.950 53.097 2072 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.68 % Allowed : 11.40 % Favored : 86.92 % 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: 0.97 (0.20), residues: 1785 helix: 2.60 (0.19), residues: 655 sheet: 1.06 (0.27), residues: 390 loop : -1.51 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 263 HIS 0.002 0.000 HIS E 133 PHE 0.036 0.001 PHE D 330 TYR 0.023 0.002 TYR A 433 ARG 0.003 0.000 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 5) link_NAG-ASN : angle 1.24019 ( 15) hydrogen bonds : bond 0.04507 ( 745) hydrogen bonds : angle 4.77418 ( 2625) SS BOND : bond 0.00388 ( 5) SS BOND : angle 0.33243 ( 10) covalent geometry : bond 0.00288 (15050) covalent geometry : angle 0.58605 (20395) *********************** 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 144 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: A 187 MET cc_start: 0.9025 (mmm) cc_final: 0.8692 (mmm) REVERT: A 263 TRP cc_start: 0.7953 (m-10) cc_final: 0.7556 (m-10) REVERT: D 113 MET cc_start: 0.8637 (ppp) cc_final: 0.8302 (pp-130) REVERT: D 221 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7654 (p90) REVERT: D 270 MET cc_start: 0.5970 (ppp) cc_final: 0.5470 (ppp) REVERT: E 113 MET cc_start: 0.8575 (ppp) cc_final: 0.8050 (ppp) REVERT: E 221 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7647 (p90) REVERT: B 187 MET cc_start: 0.9026 (mmm) cc_final: 0.8646 (mmm) REVERT: B 221 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7609 (p90) REVERT: C 178 MET cc_start: 0.9392 (ttm) cc_final: 0.9043 (ttp) REVERT: C 187 MET cc_start: 0.8946 (mmm) cc_final: 0.8361 (mmm) outliers start: 27 outliers final: 3 residues processed: 130 average time/residue: 1.2043 time to fit residues: 174.0416 Evaluate side-chains 112 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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 106 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.091920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069048 restraints weight = 34487.439| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.18 r_work: 0.2992 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15060 Z= 0.140 Angle : 0.570 8.115 20420 Z= 0.299 Chirality : 0.042 0.155 2300 Planarity : 0.003 0.034 2555 Dihedral : 4.740 21.267 2070 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.37 % Allowed : 12.09 % 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: 0.98 (0.20), residues: 1785 helix: 2.65 (0.19), residues: 655 sheet: 1.07 (0.27), residues: 390 loop : -1.54 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 263 HIS 0.003 0.001 HIS A 133 PHE 0.033 0.002 PHE A 330 TYR 0.022 0.002 TYR B 433 ARG 0.003 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 5) link_NAG-ASN : angle 1.21345 ( 15) hydrogen bonds : bond 0.04197 ( 745) hydrogen bonds : angle 4.67618 ( 2625) SS BOND : bond 0.00357 ( 5) SS BOND : angle 0.32628 ( 10) covalent geometry : bond 0.00318 (15050) covalent geometry : angle 0.56972 (20395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9062 (mmm) cc_final: 0.8613 (mmm) REVERT: A 263 TRP cc_start: 0.7956 (m-10) cc_final: 0.7566 (m-10) REVERT: D 113 MET cc_start: 0.8605 (ppp) cc_final: 0.8091 (ppp) REVERT: D 221 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7674 (p90) REVERT: D 270 MET cc_start: 0.5952 (ppp) cc_final: 0.5597 (ppp) REVERT: E 113 MET cc_start: 0.8622 (ppp) cc_final: 0.8035 (ppp) REVERT: E 221 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7643 (p90) REVERT: B 187 MET cc_start: 0.9064 (mmm) cc_final: 0.8645 (mmm) REVERT: B 221 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7573 (p90) REVERT: C 187 MET cc_start: 0.9070 (mmm) cc_final: 0.8413 (mmm) outliers start: 38 outliers final: 12 residues processed: 139 average time/residue: 1.1250 time to fit residues: 174.4302 Evaluate side-chains 122 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.091369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.068433 restraints weight = 34762.856| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.21 r_work: 0.2973 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15060 Z= 0.154 Angle : 0.576 8.746 20420 Z= 0.300 Chirality : 0.043 0.154 2300 Planarity : 0.003 0.033 2555 Dihedral : 4.739 22.067 2070 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.24 % Allowed : 11.84 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.95 (0.20), residues: 1785 helix: 2.65 (0.19), residues: 655 sheet: 0.97 (0.26), residues: 390 loop : -1.55 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 267 HIS 0.002 0.001 HIS B 133 PHE 0.037 0.002 PHE B 330 TYR 0.022 0.002 TYR B 433 ARG 0.005 0.000 ARG D 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 5) link_NAG-ASN : angle 1.19434 ( 15) hydrogen bonds : bond 0.04149 ( 745) hydrogen bonds : angle 4.65961 ( 2625) SS BOND : bond 0.00316 ( 5) SS BOND : angle 0.37703 ( 10) covalent geometry : bond 0.00354 (15050) covalent geometry : angle 0.57522 (20395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9085 (mmm) cc_final: 0.8764 (mmm) REVERT: A 263 TRP cc_start: 0.7825 (m-10) cc_final: 0.7401 (m-10) REVERT: A 334 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6892 (mp10) REVERT: D 113 MET cc_start: 0.8639 (ppp) cc_final: 0.7980 (ppp) REVERT: D 221 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7655 (p90) REVERT: D 270 MET cc_start: 0.5977 (ppp) cc_final: 0.5622 (ppp) REVERT: E 113 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8132 (ppp) REVERT: E 221 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7615 (p90) REVERT: B 187 MET cc_start: 0.9101 (mmm) cc_final: 0.8637 (mmm) REVERT: B 221 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7696 (p90) REVERT: C 187 MET cc_start: 0.9082 (mmm) cc_final: 0.8571 (mmm) outliers start: 36 outliers final: 15 residues processed: 135 average time/residue: 1.1818 time to fit residues: 177.3626 Evaluate side-chains 127 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 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 84 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 85 optimal weight: 0.0060 chunk 115 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.066840 restraints weight = 34848.985| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.19 r_work: 0.2941 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15060 Z= 0.176 Angle : 0.590 8.292 20420 Z= 0.308 Chirality : 0.043 0.151 2300 Planarity : 0.003 0.032 2555 Dihedral : 4.813 22.744 2070 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.31 % Allowed : 12.77 % 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: 0.86 (0.20), residues: 1785 helix: 2.77 (0.19), residues: 625 sheet: 0.89 (0.27), residues: 390 loop : -1.60 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 263 HIS 0.003 0.001 HIS B 239 PHE 0.026 0.002 PHE B 330 TYR 0.024 0.002 TYR A 433 ARG 0.004 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00091 ( 5) link_NAG-ASN : angle 1.35183 ( 15) hydrogen bonds : bond 0.04239 ( 745) hydrogen bonds : angle 4.66489 ( 2625) SS BOND : bond 0.00344 ( 5) SS BOND : angle 0.50261 ( 10) covalent geometry : bond 0.00407 (15050) covalent geometry : angle 0.58915 (20395) *********************** 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 to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8536 (pp-130) cc_final: 0.8173 (ppp) REVERT: A 263 TRP cc_start: 0.7851 (m-10) cc_final: 0.7269 (m-10) REVERT: D 113 MET cc_start: 0.8583 (ppp) cc_final: 0.7899 (ppp) REVERT: D 221 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7592 (p90) REVERT: D 270 MET cc_start: 0.6020 (ppp) cc_final: 0.5667 (ppp) REVERT: D 334 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6887 (mp10) REVERT: E 113 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8118 (ppp) REVERT: E 221 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7595 (p90) REVERT: B 187 MET cc_start: 0.9123 (mmm) cc_final: 0.8707 (mmm) REVERT: B 221 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7805 (p90) REVERT: C 178 MET cc_start: 0.9444 (ttm) cc_final: 0.9111 (ttp) REVERT: C 187 MET cc_start: 0.9086 (mmm) cc_final: 0.8582 (mmm) outliers start: 37 outliers final: 18 residues processed: 134 average time/residue: 1.1939 time to fit residues: 177.8433 Evaluate side-chains 132 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 416 VAL 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 D residue 334 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain 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 221 TYR Chi-restraints excluded: chain C residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 93 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 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** ** 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 = 0.3536 r_free = 0.3536 target = 0.090729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.067899 restraints weight = 34790.560| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.20 r_work: 0.2956 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15060 Z= 0.130 Angle : 0.580 9.183 20420 Z= 0.297 Chirality : 0.042 0.155 2300 Planarity : 0.003 0.031 2555 Dihedral : 4.714 22.402 2070 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.18 % Allowed : 13.40 % Favored : 84.42 % 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: 2.80 (0.19), residues: 625 sheet: 0.88 (0.27), residues: 390 loop : -1.59 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 263 HIS 0.002 0.001 HIS E 225 PHE 0.020 0.001 PHE B 330 TYR 0.021 0.002 TYR A 433 ARG 0.003 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 5) link_NAG-ASN : angle 1.03004 ( 15) hydrogen bonds : bond 0.04016 ( 745) hydrogen bonds : angle 4.55445 ( 2625) SS BOND : bond 0.00294 ( 5) SS BOND : angle 0.29239 ( 10) covalent geometry : bond 0.00294 (15050) covalent geometry : angle 0.57947 (20395) *********************** 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 151 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.7817 (m-10) cc_final: 0.7234 (m-10) REVERT: A 334 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6920 (mp10) REVERT: D 42 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8261 (mtp) REVERT: D 113 MET cc_start: 0.8579 (ppp) cc_final: 0.8055 (ppp) REVERT: D 221 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7669 (p90) REVERT: D 270 MET cc_start: 0.6074 (ppp) cc_final: 0.5741 (ppp) REVERT: D 334 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6976 (mp10) REVERT: E 113 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8104 (ppp) REVERT: E 221 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7538 (p90) REVERT: B 187 MET cc_start: 0.9113 (mmm) cc_final: 0.8773 (mmm) REVERT: B 221 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7845 (p90) REVERT: C 178 MET cc_start: 0.9433 (ttm) cc_final: 0.9102 (ttp) REVERT: C 187 MET cc_start: 0.9076 (mmm) cc_final: 0.8571 (mmm) outliers start: 35 outliers final: 22 residues processed: 139 average time/residue: 1.1303 time to fit residues: 175.4769 Evaluate side-chains 137 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.792 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 334 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 416 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 69.6334 > 50: distance: 21 - 26: 35.249 distance: 26 - 27: 33.716 distance: 27 - 28: 22.271 distance: 27 - 30: 12.623 distance: 28 - 29: 39.440 distance: 28 - 34: 24.617 distance: 30 - 31: 47.224 distance: 31 - 32: 56.486 distance: 31 - 33: 60.211 distance: 34 - 35: 48.312 distance: 35 - 36: 43.844 distance: 35 - 38: 28.165 distance: 36 - 37: 41.732 distance: 36 - 42: 34.795 distance: 38 - 39: 20.947 distance: 39 - 40: 23.240 distance: 39 - 41: 22.583 distance: 42 - 43: 12.757 distance: 42 - 173: 29.499 distance: 43 - 44: 20.903 distance: 43 - 46: 59.344 distance: 44 - 45: 47.794 distance: 44 - 53: 24.084 distance: 45 - 170: 30.623 distance: 46 - 47: 22.449 distance: 47 - 48: 28.352 distance: 47 - 49: 27.479 distance: 48 - 50: 10.863 distance: 49 - 51: 9.514 distance: 50 - 52: 8.650 distance: 51 - 52: 8.183 distance: 53 - 54: 19.867 distance: 54 - 55: 42.133 distance: 54 - 57: 17.956 distance: 55 - 56: 58.199 distance: 55 - 64: 23.497 distance: 57 - 58: 33.035 distance: 58 - 59: 35.479 distance: 58 - 60: 27.104 distance: 59 - 61: 12.454 distance: 60 - 62: 18.225 distance: 61 - 63: 8.012 distance: 62 - 63: 8.310 distance: 64 - 65: 16.069 distance: 65 - 66: 38.838 distance: 65 - 68: 50.269 distance: 66 - 67: 50.570 distance: 66 - 69: 33.468 distance: 69 - 70: 12.665 distance: 70 - 71: 24.298 distance: 70 - 73: 52.610 distance: 71 - 72: 21.399 distance: 71 - 77: 48.552 distance: 73 - 74: 16.151 distance: 74 - 75: 30.944 distance: 74 - 76: 28.167 distance: 77 - 78: 21.302 distance: 78 - 79: 48.959 distance: 78 - 81: 39.800 distance: 79 - 80: 57.911 distance: 79 - 86: 8.848 distance: 81 - 82: 52.035 distance: 82 - 83: 17.611 distance: 83 - 84: 21.114 distance: 83 - 85: 29.632 distance: 86 - 87: 32.392 distance: 86 - 126: 28.203 distance: 87 - 88: 57.273 distance: 87 - 90: 39.714 distance: 88 - 89: 25.894 distance: 88 - 95: 49.181 distance: 90 - 91: 39.541 distance: 91 - 92: 56.851 distance: 92 - 93: 50.138 distance: 93 - 94: 34.154 distance: 95 - 96: 40.919 distance: 96 - 97: 54.549 distance: 97 - 98: 14.006 distance: 97 - 99: 57.754 distance: 99 - 100: 21.808 distance: 100 - 101: 35.994 distance: 100 - 103: 32.449 distance: 101 - 102: 29.575 distance: 101 - 104: 26.420