Starting phenix.real_space_refine on Sat Aug 23 18:26:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jaf_6346/08_2025/3jaf_6346.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jaf_6346/08_2025/3jaf_6346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3jaf_6346/08_2025/3jaf_6346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jaf_6346/08_2025/3jaf_6346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jaf_6346/08_2025/3jaf_6346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jaf_6346/08_2025/3jaf_6346.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 90 5.16 5 C 9115 2.51 5 N 2210 2.21 5 O 2450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13865 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "C" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "E" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.98, per 1000 atoms: 0.21 Number of scatterers: 13865 At special positions: 0 Unit cell: (95.68, 97.76, 127.92, 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 90 16.00 O 2450 8.00 N 2210 7.00 C 9115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 632.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3270 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 41.6% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.277A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 235 through 243 removed outlier: 4.534A pdb=" N TYR A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 325 Processing helix chain 'A' and resid 328 through 363 removed outlier: 3.599A pdb=" N THR A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Proline residue: A 347 - end of helix removed outlier: 3.745A pdb=" N ILE A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 361 " --> pdb=" O TYR A 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.278A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 235 through 243 removed outlier: 4.534A pdb=" N TYR B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 325 Processing helix chain 'B' and resid 328 through 363 removed outlier: 3.599A pdb=" N THR B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Proline residue: B 347 - end of helix removed outlier: 3.745A pdb=" N ILE B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.277A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 235 through 243 removed outlier: 4.535A pdb=" N TYR C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TRP C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE C 260 " --> pdb=" O VAL C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER C 289 " --> pdb=" O GLY C 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU C 290 " --> pdb=" O SER C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 325 Processing helix chain 'C' and resid 328 through 363 removed outlier: 3.600A pdb=" N THR C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Proline residue: C 347 - end of helix removed outlier: 3.746A pdb=" N ILE C 359 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR C 360 " --> pdb=" O PHE C 356 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 361 " --> pdb=" O TYR C 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.277A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 235 through 243 removed outlier: 4.534A pdb=" N TYR D 239 " --> pdb=" O GLN D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 254 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP D 259 " --> pdb=" O TRP D 255 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 325 Processing helix chain 'D' and resid 328 through 363 removed outlier: 3.599A pdb=" N THR D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Proline residue: D 347 - end of helix removed outlier: 3.745A pdb=" N ILE D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR D 360 " --> pdb=" O PHE D 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR D 361 " --> pdb=" O TYR D 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.278A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 235 through 243 removed outlier: 4.534A pdb=" N TYR E 239 " --> pdb=" O GLN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER E 254 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP E 259 " --> pdb=" O TRP E 255 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE E 260 " --> pdb=" O VAL E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E 286 " --> pdb=" O GLN E 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER E 289 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU E 290 " --> pdb=" O SER E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 325 Processing helix chain 'E' and resid 328 through 363 removed outlier: 3.599A pdb=" N THR E 340 " --> pdb=" O LYS E 336 " (cutoff:3.500A) Proline residue: E 347 - end of helix removed outlier: 3.745A pdb=" N ILE E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR E 360 " --> pdb=" O PHE E 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR E 361 " --> pdb=" O TYR E 357 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.843A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.922A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=D, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=E, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.842A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.922A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'B' and resid 115 through 116 Processing sheet with id=H, first strand: chain 'B' and resid 115 through 116 Processing sheet with id=I, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.843A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.923A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'C' and resid 115 through 116 Processing sheet with id=L, first strand: chain 'C' and resid 115 through 116 Processing sheet with id=M, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.843A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.922A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'D' and resid 115 through 116 Processing sheet with id=P, first strand: chain 'D' and resid 115 through 116 Processing sheet with id=Q, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.843A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.923A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=T, first strand: chain 'E' and resid 115 through 116 836 hydrogen bonds defined for protein. 2418 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: 1.82 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4069 1.34 - 1.46: 2905 1.46 - 1.58: 7121 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 14245 Sorted by residual: bond pdb=" C46 IVM E 401 " pdb=" O12 IVM E 401 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C46 IVM A 503 " pdb=" O12 IVM A 503 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C46 IVM B 503 " pdb=" O12 IVM B 503 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C46 IVM D 503 " pdb=" O12 IVM D 503 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C46 IVM C 503 " pdb=" O12 IVM C 503 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 ... (remaining 14240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 17654 2.12 - 4.24: 1504 4.24 - 6.36: 228 6.36 - 8.48: 54 8.48 - 10.60: 5 Bond angle restraints: 19445 Sorted by residual: angle pdb=" N GLY B 327 " pdb=" CA GLY B 327 " pdb=" C GLY B 327 " ideal model delta sigma weight residual 111.42 122.02 -10.60 1.51e+00 4.39e-01 4.92e+01 angle pdb=" N GLY C 327 " pdb=" CA GLY C 327 " pdb=" C GLY C 327 " ideal model delta sigma weight residual 111.42 122.01 -10.59 1.51e+00 4.39e-01 4.92e+01 angle pdb=" N GLY D 327 " pdb=" CA GLY D 327 " pdb=" C GLY D 327 " ideal model delta sigma weight residual 111.42 122.00 -10.58 1.51e+00 4.39e-01 4.91e+01 angle pdb=" N GLY E 327 " pdb=" CA GLY E 327 " pdb=" C GLY E 327 " ideal model delta sigma weight residual 111.42 121.99 -10.57 1.51e+00 4.39e-01 4.90e+01 angle pdb=" N GLY A 327 " pdb=" CA GLY A 327 " pdb=" C GLY A 327 " ideal model delta sigma weight residual 111.42 121.99 -10.57 1.51e+00 4.39e-01 4.90e+01 ... (remaining 19440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.30: 8605 24.30 - 48.59: 220 48.59 - 72.89: 75 72.89 - 97.19: 40 97.19 - 121.48: 85 Dihedral angle restraints: 9025 sinusoidal: 3975 harmonic: 5050 Sorted by residual: dihedral pdb=" CB CYS E 214 " pdb=" SG CYS E 214 " pdb=" SG CYS E 225 " pdb=" CB CYS E 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.47 78.47 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS D 214 " pdb=" SG CYS D 214 " pdb=" SG CYS D 225 " pdb=" CB CYS D 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.43 78.43 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 225 " pdb=" CB CYS A 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.43 78.43 1 1.00e+01 1.00e-02 7.67e+01 ... (remaining 9022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2029 0.080 - 0.159: 250 0.159 - 0.239: 11 0.239 - 0.319: 5 0.319 - 0.399: 5 Chirality restraints: 2300 Sorted by residual: chirality pdb=" C47 IVM D 503 " pdb=" C39 IVM D 503 " pdb=" C41 IVM D 503 " pdb=" C45 IVM D 503 " both_signs ideal model delta sigma weight residual False 3.13 2.73 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C47 IVM C 503 " pdb=" C39 IVM C 503 " pdb=" C41 IVM C 503 " pdb=" C45 IVM C 503 " both_signs ideal model delta sigma weight residual False 3.13 2.73 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" C47 IVM B 503 " pdb=" C39 IVM B 503 " pdb=" C41 IVM B 503 " pdb=" C45 IVM B 503 " both_signs ideal model delta sigma weight residual False 3.13 2.73 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 2297 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 265 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO A 266 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 266 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 266 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 265 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.66e+00 pdb=" N PRO B 266 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 266 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 266 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 265 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO C 266 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 266 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 266 " -0.029 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 322 2.69 - 3.24: 14524 3.24 - 3.79: 20992 3.79 - 4.35: 28592 4.35 - 4.90: 45301 Nonbonded interactions: 109731 Sorted by model distance: nonbonded pdb=" O SER E 254 " pdb=" OG SER E 257 " model vdw 2.134 3.040 nonbonded pdb=" O SER D 254 " pdb=" OG SER D 257 " model vdw 2.134 3.040 nonbonded pdb=" O SER A 254 " pdb=" OG SER A 257 " model vdw 2.134 3.040 nonbonded pdb=" O SER B 254 " pdb=" OG SER B 257 " model vdw 2.134 3.040 nonbonded pdb=" O SER C 254 " pdb=" OG SER C 257 " model vdw 2.135 3.040 ... (remaining 109726 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue 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: 1.870 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.230 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.006 0.127 14255 Z= 0.397 Angle : 1.344 10.595 19470 Z= 0.854 Chirality : 0.056 0.399 2300 Planarity : 0.005 0.054 2360 Dihedral : 18.829 121.482 5740 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.70 % Allowed : 1.06 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.18), residues: 1700 helix: -0.70 (0.20), residues: 540 sheet: 0.76 (0.25), residues: 340 loop : -0.92 (0.18), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG C 229 TYR 0.026 0.003 TYR E 94 PHE 0.029 0.004 PHE E 29 TRP 0.023 0.003 TRP D 259 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00630 (14245) covalent geometry : angle 1.34460 (19445) SS BOND : bond 0.00709 ( 5) SS BOND : angle 0.46132 ( 10) hydrogen bonds : bond 0.14404 ( 691) hydrogen bonds : angle 9.58881 ( 2418) link_BETA1-4 : bond 0.01909 ( 5) link_BETA1-4 : angle 0.65823 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 307 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.6955 (m-30) cc_final: 0.6657 (m-30) REVERT: D 100 ASP cc_start: 0.6599 (m-30) cc_final: 0.6179 (m-30) REVERT: D 130 ASP cc_start: 0.6910 (t0) cc_final: 0.6701 (t0) REVERT: E 89 LEU cc_start: 0.8164 (mt) cc_final: 0.7915 (mt) REVERT: E 100 ASP cc_start: 0.7263 (m-30) cc_final: 0.6800 (m-30) REVERT: E 271 LEU cc_start: 0.8884 (mt) cc_final: 0.8672 (mt) outliers start: 10 outliers final: 0 residues processed: 317 average time/residue: 0.0879 time to fit residues: 43.5470 Evaluate side-chains 176 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.0980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 131 ASN A 139 ASN A 354 ASN B 54 ASN B 131 ASN B 139 ASN B 354 ASN C 54 ASN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN C 354 ASN D 54 ASN D 131 ASN D 354 ASN E 54 ASN E 131 ASN E 354 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.039755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.031797 restraints weight = 94472.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.032909 restraints weight = 54634.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.033735 restraints weight = 36727.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.034231 restraints weight = 27108.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.034706 restraints weight = 21783.664| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14255 Z= 0.183 Angle : 0.869 9.577 19470 Z= 0.421 Chirality : 0.050 0.361 2300 Planarity : 0.006 0.049 2360 Dihedral : 13.288 86.470 2745 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.32 % Allowed : 8.59 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.19), residues: 1700 helix: 0.60 (0.20), residues: 575 sheet: 0.82 (0.25), residues: 380 loop : -0.53 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 212 TYR 0.020 0.002 TYR C 144 PHE 0.027 0.002 PHE D 353 TRP 0.007 0.001 TRP E 302 HIS 0.003 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00399 (14245) covalent geometry : angle 0.86952 (19445) SS BOND : bond 0.00128 ( 5) SS BOND : angle 0.21731 ( 10) hydrogen bonds : bond 0.04898 ( 691) hydrogen bonds : angle 6.18401 ( 2418) link_BETA1-4 : bond 0.00906 ( 5) link_BETA1-4 : angle 0.56116 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.9141 (ttm110) cc_final: 0.8854 (ttp80) REVERT: A 152 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8636 (mm) REVERT: A 156 MET cc_start: 0.8494 (ptp) cc_final: 0.8219 (mtp) REVERT: A 282 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8743 (mm-40) REVERT: B 105 MET cc_start: 0.8930 (mmt) cc_final: 0.8544 (mmt) REVERT: C 72 MET cc_start: 0.9012 (tpt) cc_final: 0.8549 (tpp) REVERT: C 94 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.7028 (m-10) REVERT: C 236 MET cc_start: 0.8355 (mmm) cc_final: 0.8032 (mmp) REVERT: C 251 VAL cc_start: 0.9631 (t) cc_final: 0.9136 (t) REVERT: C 252 ILE cc_start: 0.9676 (mt) cc_final: 0.9304 (mt) REVERT: C 255 TRP cc_start: 0.8994 (m-10) cc_final: 0.8445 (m-10) REVERT: C 282 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8892 (mm-40) REVERT: D 34 MET cc_start: 0.8001 (tpp) cc_final: 0.7779 (tpp) REVERT: D 72 MET cc_start: 0.8810 (tpt) cc_final: 0.8585 (tpt) REVERT: D 101 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8784 (tp) REVERT: D 105 MET cc_start: 0.8914 (mmm) cc_final: 0.8379 (mmm) REVERT: D 152 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8894 (mm) REVERT: D 278 THR cc_start: 0.9256 (p) cc_final: 0.8895 (t) REVERT: D 282 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8753 (mm-40) REVERT: E 89 LEU cc_start: 0.9318 (mt) cc_final: 0.9023 (mt) REVERT: E 133 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8731 (pp) REVERT: E 152 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8603 (mm) REVERT: E 163 MET cc_start: 0.8907 (pmm) cc_final: 0.8676 (pmm) REVERT: E 179 MET cc_start: 0.8853 (tpp) cc_final: 0.8426 (mmm) REVERT: E 278 THR cc_start: 0.9211 (p) cc_final: 0.8876 (t) outliers start: 33 outliers final: 6 residues processed: 225 average time/residue: 0.0831 time to fit residues: 30.1852 Evaluate side-chains 170 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 132 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN B 261 ASN C 235 GLN C 261 ASN D 139 ASN D 166 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.039219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.031230 restraints weight = 95886.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.032347 restraints weight = 55682.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.033191 restraints weight = 37399.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.033777 restraints weight = 27716.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.034191 restraints weight = 21921.501| |-----------------------------------------------------------------------------| r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14255 Z= 0.199 Angle : 0.785 11.844 19470 Z= 0.387 Chirality : 0.044 0.173 2300 Planarity : 0.005 0.048 2360 Dihedral : 10.924 74.788 2745 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.90 % Allowed : 13.52 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.20), residues: 1700 helix: 1.21 (0.21), residues: 575 sheet: 0.70 (0.26), residues: 385 loop : -0.45 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 287 TYR 0.021 0.002 TYR A 144 PHE 0.021 0.002 PHE D 353 TRP 0.005 0.001 TRP B 358 HIS 0.004 0.002 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00429 (14245) covalent geometry : angle 0.78442 (19445) SS BOND : bond 0.00043 ( 5) SS BOND : angle 0.42604 ( 10) hydrogen bonds : bond 0.04497 ( 691) hydrogen bonds : angle 5.63165 ( 2418) link_BETA1-4 : bond 0.00608 ( 5) link_BETA1-4 : angle 1.30646 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8047 (tpp) cc_final: 0.7642 (tpp) REVERT: A 101 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8710 (tp) REVERT: A 105 MET cc_start: 0.8930 (mmm) cc_final: 0.8248 (mmm) REVERT: A 152 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8747 (mm) REVERT: A 156 MET cc_start: 0.8568 (ptp) cc_final: 0.8335 (mtp) REVERT: A 282 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8861 (mm-40) REVERT: A 346 PHE cc_start: 0.8738 (m-80) cc_final: 0.8372 (m-80) REVERT: B 72 MET cc_start: 0.9022 (tpp) cc_final: 0.8764 (tpp) REVERT: B 101 LEU cc_start: 0.8645 (tp) cc_final: 0.8355 (tp) REVERT: B 179 MET cc_start: 0.9052 (tpp) cc_final: 0.8509 (mmm) REVERT: B 244 TYR cc_start: 0.9132 (m-80) cc_final: 0.8719 (m-80) REVERT: B 303 MET cc_start: 0.9545 (mmm) cc_final: 0.9325 (mmm) REVERT: C 72 MET cc_start: 0.9023 (tpt) cc_final: 0.8717 (tpt) REVERT: C 101 LEU cc_start: 0.8760 (tp) cc_final: 0.8537 (tp) REVERT: C 179 MET cc_start: 0.8961 (tpp) cc_final: 0.8364 (mmm) REVERT: C 204 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8760 (mm) REVERT: C 282 GLN cc_start: 0.9302 (mm-40) cc_final: 0.8972 (mm-40) REVERT: D 72 MET cc_start: 0.8882 (tpt) cc_final: 0.8645 (tpt) REVERT: D 152 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8812 (mm) REVERT: D 156 MET cc_start: 0.7672 (ptt) cc_final: 0.7463 (ptt) REVERT: D 236 MET cc_start: 0.8318 (mmm) cc_final: 0.7984 (tpp) REVERT: D 278 THR cc_start: 0.9369 (p) cc_final: 0.8862 (t) REVERT: D 282 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8795 (mm-40) REVERT: E 34 MET cc_start: 0.7957 (tpp) cc_final: 0.7734 (tpp) REVERT: E 75 ARG cc_start: 0.9087 (ttm110) cc_final: 0.8707 (ttm-80) REVERT: E 89 LEU cc_start: 0.9282 (mt) cc_final: 0.8846 (mt) REVERT: E 101 LEU cc_start: 0.8930 (tp) cc_final: 0.8715 (tp) REVERT: E 163 MET cc_start: 0.8771 (pmm) cc_final: 0.8554 (pmm) REVERT: E 179 MET cc_start: 0.8818 (tpp) cc_final: 0.8492 (mmm) REVERT: E 278 THR cc_start: 0.9240 (p) cc_final: 0.8973 (t) outliers start: 27 outliers final: 14 residues processed: 188 average time/residue: 0.0843 time to fit residues: 24.8406 Evaluate side-chains 168 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.0238 > 50: distance: 45 - 63: 36.454 distance: 49 - 70: 34.213 distance: 53 - 75: 37.263 distance: 58 - 63: 35.379 distance: 63 - 64: 40.208 distance: 64 - 67: 39.941 distance: 65 - 66: 38.888 distance: 65 - 70: 39.436 distance: 67 - 69: 39.727 distance: 70 - 71: 57.202 distance: 71 - 72: 40.225 distance: 71 - 74: 55.168 distance: 72 - 75: 55.999 distance: 75 - 76: 56.063 distance: 76 - 77: 41.019 distance: 77 - 78: 38.802 distance: 77 - 86: 40.787 distance: 78 - 108: 70.106 distance: 86 - 87: 28.877 distance: 87 - 88: 12.780 distance: 87 - 90: 29.268 distance: 88 - 89: 39.898 distance: 89 - 119: 39.974 distance: 94 - 97: 39.321 distance: 95 - 96: 40.313 distance: 96 - 127: 54.385 distance: 98 - 99: 41.011 distance: 98 - 100: 39.701 distance: 101 - 102: 39.330 distance: 102 - 103: 41.186 distance: 104 - 135: 54.332 distance: 105 - 106: 39.905 distance: 109 - 112: 39.447 distance: 111 - 146: 33.653 distance: 112 - 113: 40.310 distance: 113 - 114: 39.814 distance: 113 - 115: 39.303 distance: 116 - 118: 56.505 distance: 119 - 120: 69.598 distance: 120 - 121: 55.450 distance: 120 - 123: 40.514 distance: 121 - 122: 57.088 distance: 122 - 153: 33.385 distance: 123 - 124: 39.558 distance: 124 - 125: 39.895 distance: 124 - 126: 57.553 distance: 128 - 129: 41.342 distance: 128 - 131: 39.094 distance: 130 - 161: 37.459 distance: 131 - 132: 39.847 distance: 131 - 133: 38.804 distance: 135 - 136: 39.198 distance: 136 - 137: 56.840 distance: 136 - 139: 39.624 distance: 137 - 138: 30.406 distance: 137 - 146: 35.239 distance: 138 - 168: 28.430 distance: 140 - 142: 39.068 distance: 144 - 145: 40.280