Starting phenix.real_space_refine on Fri Jul 3 18:03:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22rj_68620/07_2026/22rj_68620_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/22rj_68620/07_2026/22rj_68620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22rj_68620/07_2026/22rj_68620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22rj_68620/07_2026/22rj_68620.map" model { file = "/net/cci-nas-00/data/ceres_data/22rj_68620/07_2026/22rj_68620_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22rj_68620/07_2026/22rj_68620_neut.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 80 5.16 5 C 9652 2.51 5 N 2480 2.21 5 O 2736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14952 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2621 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 319} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2621 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 319} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2621 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 319} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2621 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 319} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1116 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1116 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1116 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1116 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' K': 4} Chain breaks: 4 Time building chain proxies: 3.19, per 1000 atoms: 0.21 Number of scatterers: 14952 At special positions: 0 Unit cell: (115.75, 115.75, 123.158, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 80 16.00 O 2736 8.00 N 2480 7.00 C 9652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 598.1 milliseconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 79.6% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 124 through 143 Processing helix chain 'A' and resid 150 through 179 Processing helix chain 'A' and resid 180 through 185 removed outlier: 6.216A pdb=" N ARG A 183 " --> pdb=" O CYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 194 Processing helix chain 'A' and resid 196 through 210 removed outlier: 3.658A pdb=" N VAL A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 227 through 239 removed outlier: 4.710A pdb=" N ILE A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 257 Processing helix chain 'A' and resid 257 through 284 Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.543A pdb=" N ALA A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 365 removed outlier: 4.718A pdb=" N SER A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 372 through 388 Processing helix chain 'A' and resid 517 through 537 Processing helix chain 'A' and resid 542 through 573 removed outlier: 3.895A pdb=" N VAL A 546 " --> pdb=" O ASP A 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 124 through 143 Processing helix chain 'B' and resid 150 through 179 Processing helix chain 'B' and resid 180 through 185 removed outlier: 6.164A pdb=" N ARG B 183 " --> pdb=" O CYS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 194 Processing helix chain 'B' and resid 196 through 210 removed outlier: 3.656A pdb=" N VAL B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 227 through 239 removed outlier: 4.714A pdb=" N ILE B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 235 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 257 Processing helix chain 'B' and resid 257 through 284 Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.543A pdb=" N ALA B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 365 removed outlier: 4.722A pdb=" N SER B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 372 through 388 Processing helix chain 'B' and resid 517 through 539 removed outlier: 3.932A pdb=" N ARG B 539 " --> pdb=" O LYS B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 573 removed outlier: 3.912A pdb=" N VAL B 546 " --> pdb=" O ASP B 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 124 through 143 Processing helix chain 'C' and resid 150 through 179 Processing helix chain 'C' and resid 180 through 185 removed outlier: 6.167A pdb=" N ARG C 183 " --> pdb=" O CYS C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 194 Processing helix chain 'C' and resid 196 through 210 removed outlier: 3.658A pdb=" N VAL C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 Processing helix chain 'C' and resid 227 through 239 removed outlier: 4.708A pdb=" N ILE C 234 " --> pdb=" O ARG C 230 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 235 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 257 Processing helix chain 'C' and resid 257 through 284 Processing helix chain 'C' and resid 302 through 315 removed outlier: 3.542A pdb=" N ALA C 306 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 365 removed outlier: 4.721A pdb=" N SER C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 372 through 388 Processing helix chain 'C' and resid 517 through 539 removed outlier: 3.942A pdb=" N ARG C 539 " --> pdb=" O LYS C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 573 removed outlier: 3.890A pdb=" N VAL C 546 " --> pdb=" O ASP C 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 116 Processing helix chain 'D' and resid 124 through 143 Processing helix chain 'D' and resid 150 through 179 Processing helix chain 'D' and resid 180 through 185 removed outlier: 6.210A pdb=" N ARG D 183 " --> pdb=" O CYS D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 194 Processing helix chain 'D' and resid 196 through 210 removed outlier: 3.657A pdb=" N VAL D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'D' and resid 227 through 239 removed outlier: 4.709A pdb=" N ILE D 234 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU D 235 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 257 Processing helix chain 'D' and resid 257 through 284 Processing helix chain 'D' and resid 302 through 315 removed outlier: 3.542A pdb=" N ALA D 306 " --> pdb=" O THR D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 365 removed outlier: 4.718A pdb=" N SER D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 371 through 388 removed outlier: 4.716A pdb=" N ALA D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 537 Processing helix chain 'D' and resid 542 through 573 removed outlier: 3.902A pdb=" N VAL D 546 " --> pdb=" O ASP D 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 29 through 41 removed outlier: 3.739A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU E 40 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.515A pdb=" N LEU E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 74 Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 82 through 92 removed outlier: 3.694A pdb=" N VAL E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 39 removed outlier: 3.867A pdb=" N LEU F 33 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG F 38 " --> pdb=" O GLY F 34 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER F 39 " --> pdb=" O THR F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 57 removed outlier: 3.572A pdb=" N LEU F 49 " --> pdb=" O THR F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 74 Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.517A pdb=" N VAL F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'G' and resid 7 through 21 Processing helix chain 'G' and resid 29 through 39 removed outlier: 3.856A pdb=" N LEU G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER G 39 " --> pdb=" O THR G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 57 removed outlier: 3.582A pdb=" N LEU G 49 " --> pdb=" O THR G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 74 Processing helix chain 'G' and resid 76 through 80 Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.514A pdb=" N VAL G 92 " --> pdb=" O GLU G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 111 Processing helix chain 'G' and resid 118 through 130 Processing helix chain 'G' and resid 139 through 147 Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.663A pdb=" N LEU H 33 " --> pdb=" O THR H 29 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 57 removed outlier: 3.615A pdb=" N LEU H 49 " --> pdb=" O THR H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 74 Processing helix chain 'H' and resid 76 through 81 removed outlier: 4.170A pdb=" N ASP H 81 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.682A pdb=" N VAL H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 139 through 145 Processing sheet with id=AA1, first strand: chain 'E' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AA4, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'G' and resid 27 through 28 Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'H' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'H' and resid 100 through 102 1066 hydrogen bonds defined for protein. 3138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2488 1.31 - 1.44: 4088 1.44 - 1.56: 8523 1.56 - 1.69: 1 1.69 - 1.81: 136 Bond restraints: 15236 Sorted by residual: bond pdb=" C TRP B 265 " pdb=" O TRP B 265 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.26e-02 6.30e+03 1.33e+01 bond pdb=" C TRP C 265 " pdb=" O TRP C 265 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.26e-02 6.30e+03 1.27e+01 bond pdb=" C TRP A 265 " pdb=" O TRP A 265 " ideal model delta sigma weight residual 1.236 1.192 0.045 1.26e-02 6.30e+03 1.25e+01 bond pdb=" C TRP D 265 " pdb=" O TRP D 265 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.26e-02 6.30e+03 1.24e+01 bond pdb=" CA TRP B 265 " pdb=" C TRP B 265 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.35e-02 5.49e+03 9.81e+00 ... (remaining 15231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 19880 1.64 - 3.28: 564 3.28 - 4.91: 105 4.91 - 6.55: 25 6.55 - 8.19: 10 Bond angle restraints: 20584 Sorted by residual: angle pdb=" CA TYR D 541 " pdb=" CB TYR D 541 " pdb=" CG TYR D 541 " ideal model delta sigma weight residual 113.90 122.09 -8.19 1.80e+00 3.09e-01 2.07e+01 angle pdb=" CA TYR A 541 " pdb=" CB TYR A 541 " pdb=" CG TYR A 541 " ideal model delta sigma weight residual 113.90 122.02 -8.12 1.80e+00 3.09e-01 2.03e+01 angle pdb=" CA TYR B 541 " pdb=" CB TYR B 541 " pdb=" CG TYR B 541 " ideal model delta sigma weight residual 113.90 121.94 -8.04 1.80e+00 3.09e-01 1.99e+01 angle pdb=" CA TYR C 541 " pdb=" CB TYR C 541 " pdb=" CG TYR C 541 " ideal model delta sigma weight residual 113.90 121.92 -8.02 1.80e+00 3.09e-01 1.99e+01 angle pdb=" N GLN D 526 " pdb=" CA GLN D 526 " pdb=" C GLN D 526 " ideal model delta sigma weight residual 111.28 106.57 4.71 1.09e+00 8.42e-01 1.86e+01 ... (remaining 20579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 7920 16.23 - 32.47: 833 32.47 - 48.70: 231 48.70 - 64.93: 22 64.93 - 81.16: 6 Dihedral angle restraints: 9012 sinusoidal: 3580 harmonic: 5432 Sorted by residual: dihedral pdb=" CA LEU A 226 " pdb=" C LEU A 226 " pdb=" N ARG A 227 " pdb=" CA ARG A 227 " ideal model delta harmonic sigma weight residual -180.00 -157.48 -22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LEU B 226 " pdb=" C LEU B 226 " pdb=" N ARG B 227 " pdb=" CA ARG B 227 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LEU D 226 " pdb=" C LEU D 226 " pdb=" N ARG D 227 " pdb=" CA ARG D 227 " ideal model delta harmonic sigma weight residual 180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 9009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1403 0.031 - 0.063: 653 0.063 - 0.094: 200 0.094 - 0.125: 66 0.125 - 0.157: 10 Chirality restraints: 2332 Sorted by residual: chirality pdb=" CA GLN F 144 " pdb=" N GLN F 144 " pdb=" C GLN F 144 " pdb=" CB GLN F 144 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA GLN G 144 " pdb=" N GLN G 144 " pdb=" C GLN G 144 " pdb=" CB GLN G 144 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CB ILE E 64 " pdb=" CA ILE E 64 " pdb=" CG1 ILE E 64 " pdb=" CG2 ILE E 64 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 2329 not shown) Planarity restraints: 2588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 541 " 0.023 2.00e-02 2.50e+03 1.47e-02 4.34e+00 pdb=" CG TYR B 541 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 541 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 541 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 541 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 541 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 541 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 541 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 66 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO E 67 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 541 " -0.019 2.00e-02 2.50e+03 1.36e-02 3.68e+00 pdb=" CG TYR D 541 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR D 541 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR D 541 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 541 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 541 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 541 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 541 " -0.004 2.00e-02 2.50e+03 ... (remaining 2585 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 3533 2.78 - 3.37: 17928 3.37 - 3.96: 28758 3.96 - 4.55: 40068 4.55 - 5.14: 57635 Nonbonded interactions: 147922 Sorted by model distance: nonbonded pdb=" O GLU H 46 " pdb=" NE2 GLN H 50 " model vdw 2.190 3.120 nonbonded pdb=" OD2 ASP F 134 " pdb=" NE2 GLN F 136 " model vdw 2.249 3.120 nonbonded pdb=" OD2 ASP G 134 " pdb=" NE2 GLN G 136 " model vdw 2.250 3.120 nonbonded pdb=" OD2 ASP H 134 " pdb=" NE2 GLN H 136 " model vdw 2.259 3.120 nonbonded pdb=" OD2 ASP E 134 " pdb=" NE2 GLN E 136 " model vdw 2.267 3.120 ... (remaining 147917 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 103 through 573) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.630 Find NCS groups from input model: 0.270 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:9.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 : 0.005 0.046 15236 Z= 0.265 Angle : 0.723 8.188 20584 Z= 0.426 Chirality : 0.041 0.157 2332 Planarity : 0.004 0.048 2588 Dihedral : 14.279 81.164 5508 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.06 % Allowed : 5.52 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.17), residues: 1840 helix: -1.53 (0.12), residues: 1392 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 567 TYR 0.034 0.002 TYR B 541 PHE 0.011 0.002 PHE G 142 TRP 0.009 0.001 TRP A 308 HIS 0.007 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.27 (15236) covalent geometry : angle 0.72264 / 0.43 (20584) hydrogen bonds : bond 0.12378 / 8.13 ( 1066) hydrogen bonds : angle 5.80299 / 4.13 ( 3138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 409 time to evaluate : 0.526 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: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.7132 (ttp80) cc_final: 0.6639 (tmt-80) REVERT: A 192 LYS cc_start: 0.8863 (mptt) cc_final: 0.8561 (mmtt) REVERT: A 377 GLU cc_start: 0.7738 (tp30) cc_final: 0.7207 (tp30) REVERT: A 542 ASP cc_start: 0.8556 (t0) cc_final: 0.8271 (t70) REVERT: B 117 ARG cc_start: 0.7148 (ttp80) cc_final: 0.6649 (tmt-80) REVERT: B 192 LYS cc_start: 0.8851 (mptt) cc_final: 0.8592 (mmtt) REVERT: B 377 GLU cc_start: 0.8014 (tp30) cc_final: 0.6919 (tp30) REVERT: B 530 TYR cc_start: 0.8975 (m-10) cc_final: 0.8733 (m-80) REVERT: B 542 ASP cc_start: 0.8584 (t0) cc_final: 0.8271 (t70) REVERT: C 117 ARG cc_start: 0.7145 (ttp80) cc_final: 0.6648 (tmt-80) REVERT: C 192 LYS cc_start: 0.8865 (mptt) cc_final: 0.8562 (mmtt) REVERT: C 377 GLU cc_start: 0.7967 (tp30) cc_final: 0.7423 (tp30) REVERT: C 530 TYR cc_start: 0.8976 (m-10) cc_final: 0.8726 (m-80) REVERT: C 542 ASP cc_start: 0.8539 (t0) cc_final: 0.8290 (t70) REVERT: D 117 ARG cc_start: 0.7149 (ttp80) cc_final: 0.6650 (tmt-80) REVERT: D 192 LYS cc_start: 0.8866 (mptt) cc_final: 0.8558 (mmtt) REVERT: D 542 ASP cc_start: 0.8536 (t0) cc_final: 0.8253 (t70) REVERT: E 37 MET cc_start: 0.8108 (mtt) cc_final: 0.7421 (mtt) REVERT: E 116 LYS cc_start: 0.8430 (mttt) cc_final: 0.8179 (mppt) REVERT: E 138 ASN cc_start: 0.3276 (t0) cc_final: 0.2220 (t0) REVERT: E 146 MET cc_start: 0.5916 (tpp) cc_final: 0.5274 (mmm) REVERT: F 13 PHE cc_start: 0.6779 (m-10) cc_final: 0.5973 (m-10) REVERT: F 146 MET cc_start: 0.5121 (tpt) cc_final: 0.4889 (ttt) REVERT: G 13 PHE cc_start: 0.6678 (m-10) cc_final: 0.5828 (m-10) REVERT: G 37 MET cc_start: 0.8322 (mtt) cc_final: 0.8058 (mtt) REVERT: G 146 MET cc_start: 0.5139 (tpt) cc_final: 0.4829 (ttt) REVERT: H 116 LYS cc_start: 0.8528 (mttt) cc_final: 0.8261 (mppt) REVERT: H 146 MET cc_start: 0.6276 (tpp) cc_final: 0.5716 (mmm) outliers start: 1 outliers final: 4 residues processed: 410 average time/residue: 0.5328 time to fit residues: 240.9952 Evaluate side-chains 340 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 336 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain D residue 563 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 HIS B 257 HIS C 257 HIS D 257 HIS E 98 ASN E 144 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 ASN H 98 ASN H 112 ASN H 144 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.222669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135396 restraints weight = 21263.365| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.82 r_work: 0.3214 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15236 Z= 0.163 Angle : 0.652 9.437 20584 Z= 0.338 Chirality : 0.038 0.197 2332 Planarity : 0.004 0.042 2588 Dihedral : 5.305 90.936 2053 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.96 % Allowed : 14.42 % Favored : 81.62 % 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 are not related in a simple way. whole: -0.56 (0.19), residues: 1840 helix: 0.17 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -2.05 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 75 TYR 0.034 0.002 TYR A 530 PHE 0.025 0.002 PHE H 69 TRP 0.009 0.001 TRP C 308 HIS 0.002 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (15236) covalent geometry : angle 0.65208 / 0.34 (20584) hydrogen bonds : bond 0.04417 / 2.97 ( 1066) hydrogen bonds : angle 4.51173 / 3.18 ( 3138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 355 time to evaluate : 0.506 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.7417 (ttp80) cc_final: 0.7112 (tmt-80) REVERT: A 365 GLN cc_start: 0.5972 (tm-30) cc_final: 0.5770 (tm-30) REVERT: A 380 GLN cc_start: 0.7690 (mt0) cc_final: 0.7439 (mt0) REVERT: A 542 ASP cc_start: 0.8542 (t0) cc_final: 0.8158 (t0) REVERT: B 117 ARG cc_start: 0.7363 (ttp80) cc_final: 0.7050 (tmt-80) REVERT: B 365 GLN cc_start: 0.6025 (tt0) cc_final: 0.5789 (tm-30) REVERT: B 377 GLU cc_start: 0.8269 (tp30) cc_final: 0.7730 (tp30) REVERT: B 380 GLN cc_start: 0.7840 (mt0) cc_final: 0.7385 (mt0) REVERT: B 542 ASP cc_start: 0.8718 (t0) cc_final: 0.8337 (t70) REVERT: C 117 ARG cc_start: 0.7418 (ttp80) cc_final: 0.7113 (tmt-80) REVERT: C 542 ASP cc_start: 0.8500 (t0) cc_final: 0.8194 (t0) REVERT: D 117 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7109 (tmt-80) REVERT: D 365 GLN cc_start: 0.6014 (tm-30) cc_final: 0.5809 (tm-30) REVERT: D 542 ASP cc_start: 0.8522 (t0) cc_final: 0.8119 (t0) REVERT: E 72 MET cc_start: 0.8590 (mmm) cc_final: 0.8327 (mpp) REVERT: E 77 MET cc_start: 0.8106 (mmp) cc_final: 0.7857 (mmp) REVERT: E 141 GLU cc_start: 0.8562 (pm20) cc_final: 0.8224 (pm20) REVERT: F 77 MET cc_start: 0.8175 (mmp) cc_final: 0.7796 (mmp) REVERT: G 110 MET cc_start: 0.7669 (mtp) cc_final: 0.7153 (mmt) REVERT: G 139 TYR cc_start: 0.7828 (p90) cc_final: 0.7442 (p90) REVERT: H 146 MET cc_start: 0.6431 (tpp) cc_final: 0.5648 (mmm) outliers start: 61 outliers final: 25 residues processed: 378 average time/residue: 0.5150 time to fit residues: 215.9485 Evaluate side-chains 345 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 320 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 144 GLN Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 144 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 75 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 380 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 112 ASN E 144 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN G 112 ASN ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN H 112 ASN H 144 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.222255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.129500 restraints weight = 21517.959| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.94 r_work: 0.3317 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15236 Z= 0.156 Angle : 0.665 9.548 20584 Z= 0.338 Chirality : 0.039 0.196 2332 Planarity : 0.004 0.034 2588 Dihedral : 4.549 24.832 2050 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.90 % Allowed : 18.38 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1840 helix: 1.01 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : -1.47 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 75 TYR 0.027 0.001 TYR C 530 PHE 0.010 0.001 PHE H 69 TRP 0.009 0.001 TRP B 308 HIS 0.002 0.000 HIS G 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (15236) covalent geometry : angle 0.66459 / 0.34 (20584) hydrogen bonds : bond 0.04276 / 2.87 ( 1066) hydrogen bonds : angle 4.28636 / 3.00 ( 3138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 334 time to evaluate : 0.643 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: symmetry clash REVERT: A 362 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7824 (mt0) REVERT: A 542 ASP cc_start: 0.8521 (t0) cc_final: 0.8221 (t70) REVERT: B 362 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7831 (mt0) REVERT: B 380 GLN cc_start: 0.7849 (mt0) cc_final: 0.7508 (mt0) REVERT: B 542 ASP cc_start: 0.8431 (t0) cc_final: 0.8226 (t70) REVERT: C 117 ARG cc_start: 0.7414 (ttp80) cc_final: 0.7112 (tmt-80) REVERT: C 362 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7750 (mt0) REVERT: C 542 ASP cc_start: 0.8430 (t0) cc_final: 0.8148 (t0) REVERT: D 117 ARG cc_start: 0.7419 (ttp80) cc_final: 0.7116 (tmt-80) REVERT: D 362 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: D 542 ASP cc_start: 0.8537 (t0) cc_final: 0.8241 (t70) REVERT: E 72 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7739 (mmm) REVERT: F 79 ASP cc_start: 0.8275 (m-30) cc_final: 0.7648 (t70) REVERT: F 90 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: F 98 ASN cc_start: 0.6744 (p0) cc_final: 0.6135 (p0) REVERT: F 117 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7848 (mt) REVERT: G 73 MET cc_start: 0.8266 (ttp) cc_final: 0.8038 (ttp) REVERT: G 75 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7140 (tmm160) REVERT: G 76 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8088 (tptt) REVERT: G 98 ASN cc_start: 0.6737 (p0) cc_final: 0.6305 (p0) REVERT: H 50 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8367 (mm-40) outliers start: 60 outliers final: 16 residues processed: 354 average time/residue: 0.4936 time to fit residues: 195.4358 Evaluate side-chains 318 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 294 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 144 GLN Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 50 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 170 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 175 optimal weight: 0.0570 chunk 145 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 380 GLN C 380 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 112 ASN E 144 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.222811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140408 restraints weight = 21419.917| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.59 r_work: 0.3262 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15236 Z= 0.144 Angle : 0.669 9.526 20584 Z= 0.336 Chirality : 0.038 0.145 2332 Planarity : 0.003 0.029 2588 Dihedral : 4.265 24.410 2046 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.74 % Allowed : 19.81 % Favored : 75.45 % 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 are not related in a simple way. whole: 1.12 (0.20), residues: 1840 helix: 1.33 (0.14), residues: 1412 sheet: None (None), residues: 0 loop : -1.13 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 75 TYR 0.031 0.001 TYR B 530 PHE 0.016 0.001 PHE G 13 TRP 0.022 0.001 TRP B 176 HIS 0.002 0.000 HIS F 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (15236) covalent geometry : angle 0.66948 / 0.34 (20584) hydrogen bonds : bond 0.04061 / 2.71 ( 1066) hydrogen bonds : angle 4.19094 / 2.95 ( 3138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 318 time to evaluate : 0.654 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: A 362 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7732 (mt0) REVERT: A 380 GLN cc_start: 0.7793 (mt0) cc_final: 0.7593 (mt0) REVERT: A 526 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8056 (tm-30) REVERT: A 527 PHE cc_start: 0.9288 (t80) cc_final: 0.9065 (t80) REVERT: A 542 ASP cc_start: 0.8403 (t0) cc_final: 0.8120 (t70) REVERT: B 240 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7863 (tpt) REVERT: B 362 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: B 380 GLN cc_start: 0.7772 (mt0) cc_final: 0.7493 (mt0) REVERT: B 542 ASP cc_start: 0.8358 (t0) cc_final: 0.8102 (t70) REVERT: C 117 ARG cc_start: 0.7337 (ttp80) cc_final: 0.7071 (tmt-80) REVERT: C 362 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: D 117 ARG cc_start: 0.7303 (ttp80) cc_final: 0.7036 (tmt-80) REVERT: D 362 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: D 526 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8508 (tp-100) REVERT: D 542 ASP cc_start: 0.8308 (t0) cc_final: 0.8002 (t0) REVERT: E 37 MET cc_start: 0.8750 (mtt) cc_final: 0.8512 (ptp) REVERT: E 98 ASN cc_start: 0.4223 (OUTLIER) cc_final: 0.3642 (p0) REVERT: E 109 VAL cc_start: 0.8528 (m) cc_final: 0.8243 (p) REVERT: F 73 MET cc_start: 0.8445 (ttp) cc_final: 0.7605 (ttt) REVERT: F 75 ARG cc_start: 0.7816 (tmm160) cc_final: 0.7559 (tmm160) REVERT: F 76 LYS cc_start: 0.8527 (mmmt) cc_final: 0.8088 (tptt) REVERT: F 79 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7537 (t70) REVERT: F 90 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: F 98 ASN cc_start: 0.6468 (p0) cc_final: 0.5895 (p0) REVERT: G 20 PHE cc_start: 0.7192 (m-80) cc_final: 0.6975 (t80) REVERT: G 79 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7445 (t70) REVERT: G 87 ARG cc_start: 0.8440 (mtm110) cc_final: 0.8148 (mtm110) REVERT: G 90 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: G 98 ASN cc_start: 0.6603 (p0) cc_final: 0.6022 (p0) REVERT: G 139 TYR cc_start: 0.7956 (p90) cc_final: 0.7368 (p90) REVERT: H 52 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7039 (ttm) REVERT: H 138 ASN cc_start: 0.6047 (m-40) cc_final: 0.5566 (m-40) REVERT: H 141 GLU cc_start: 0.8447 (pm20) cc_final: 0.8129 (pm20) outliers start: 73 outliers final: 21 residues processed: 349 average time/residue: 0.4741 time to fit residues: 185.9382 Evaluate side-chains 325 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 291 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain D residue 526 GLN Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 90 PHE Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 52 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.9008 > 50: distance: 32 - 53: 13.972 distance: 40 - 62: 25.835 distance: 44 - 73: 12.234 distance: 47 - 53: 13.666 distance: 53 - 54: 15.864 distance: 54 - 55: 40.182 distance: 54 - 57: 9.768 distance: 55 - 56: 27.553 distance: 55 - 62: 33.441 distance: 57 - 58: 10.575 distance: 58 - 59: 20.113 distance: 59 - 60: 18.965 distance: 60 - 61: 32.216 distance: 62 - 63: 23.527 distance: 63 - 64: 15.623 distance: 63 - 66: 20.223 distance: 64 - 65: 21.291 distance: 64 - 73: 27.420 distance: 66 - 67: 11.435 distance: 67 - 68: 5.270 distance: 67 - 69: 12.710 distance: 68 - 70: 10.952 distance: 69 - 71: 3.604 distance: 70 - 72: 12.366 distance: 71 - 72: 7.347 distance: 73 - 74: 28.236 distance: 74 - 75: 21.805 distance: 74 - 77: 15.288 distance: 75 - 76: 25.271 distance: 75 - 78: 35.024 distance: 78 - 79: 16.205 distance: 79 - 80: 38.326 distance: 79 - 82: 18.865 distance: 80 - 81: 28.390 distance: 80 - 89: 24.596 distance: 82 - 83: 27.999 distance: 83 - 84: 31.973 distance: 84 - 85: 13.120 distance: 85 - 86: 17.320 distance: 86 - 87: 9.254 distance: 86 - 88: 9.060 distance: 89 - 90: 15.348 distance: 90 - 91: 33.944 distance: 90 - 93: 12.904 distance: 91 - 92: 38.840 distance: 91 - 98: 34.983 distance: 92 - 119: 42.133 distance: 93 - 94: 41.870 distance: 94 - 95: 42.352 distance: 95 - 96: 37.494 distance: 96 - 97: 13.673 distance: 98 - 99: 38.206 distance: 98 - 104: 11.494 distance: 99 - 100: 17.234 distance: 99 - 102: 56.222 distance: 100 - 101: 29.991 distance: 100 - 105: 40.459 distance: 101 - 127: 30.390 distance: 102 - 103: 6.158 distance: 103 - 104: 51.709 distance: 105 - 106: 26.093 distance: 106 - 107: 15.338 distance: 106 - 109: 11.690 distance: 107 - 108: 30.120 distance: 107 - 113: 25.934 distance: 108 - 135: 20.199 distance: 109 - 110: 29.486 distance: 110 - 111: 25.493 distance: 110 - 112: 10.068 distance: 113 - 114: 23.783 distance: 114 - 115: 22.438 distance: 114 - 117: 10.996 distance: 115 - 116: 30.899 distance: 115 - 119: 36.491 distance: 116 - 142: 18.609 distance: 117 - 118: 8.153 distance: 119 - 120: 24.225 distance: 120 - 121: 26.412 distance: 120 - 123: 10.912 distance: 121 - 122: 30.053 distance: 121 - 127: 28.349 distance: 122 - 150: 23.224 distance: 123 - 124: 14.896 distance: 124 - 125: 14.495 distance: 127 - 128: 20.979 distance: 128 - 129: 32.000 distance: 128 - 131: 12.909 distance: 129 - 130: 15.693 distance: 129 - 135: 21.573 distance: 130 - 161: 15.549 distance: 131 - 132: 8.574 distance: 132 - 133: 13.591 distance: 132 - 134: 27.309