Starting phenix.real_space_refine on Fri May 16 15:41:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4r_47518/05_2025/9e4r_47518.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4r_47518/05_2025/9e4r_47518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e4r_47518/05_2025/9e4r_47518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4r_47518/05_2025/9e4r_47518.map" model { file = "/net/cci-nas-00/data/ceres_data/9e4r_47518/05_2025/9e4r_47518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4r_47518/05_2025/9e4r_47518.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 Fe 6 7.16 5 S 60 5.16 5 C 9384 2.51 5 N 2502 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14784 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2421 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 294} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 4.83, per 1000 atoms: 0.33 Number of scatterers: 14784 At special positions: 0 Unit cell: (102.83, 99.19, 95.55, 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) Fe 6 26.01 S 60 16.00 O 2832 8.00 N 2502 7.00 C 9384 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.9 seconds 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3396 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 30 sheets defined 39.2% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 31 through 55 removed outlier: 3.699A pdb=" N GLU A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER A 46 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.876A pdb=" N CYS A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 265 through 278 removed outlier: 4.357A pdb=" N ILE A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 31 through 55 removed outlier: 3.699A pdb=" N GLU B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER B 46 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG B 55 " --> pdb=" O GLY B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 111 through 127 removed outlier: 3.876A pdb=" N CYS B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 167 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 265 through 278 removed outlier: 4.357A pdb=" N ILE B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'C' and resid 10 through 16 Processing helix chain 'C' and resid 31 through 55 removed outlier: 3.700A pdb=" N GLU C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER C 46 " --> pdb=" O CYS C 42 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 111 through 127 removed outlier: 3.876A pdb=" N CYS C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 167 Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 265 through 278 removed outlier: 4.356A pdb=" N ILE C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 304 through 310 Processing helix chain 'D' and resid 10 through 16 Processing helix chain 'D' and resid 31 through 55 removed outlier: 3.699A pdb=" N GLU D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER D 46 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 76 Processing helix chain 'D' and resid 111 through 127 removed outlier: 3.877A pdb=" N CYS D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 167 Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 189 through 196 Processing helix chain 'D' and resid 197 through 206 Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 265 through 278 removed outlier: 4.357A pdb=" N ILE D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 304 through 310 Processing helix chain 'E' and resid 10 through 16 Processing helix chain 'E' and resid 31 through 55 removed outlier: 3.699A pdb=" N GLU E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER E 46 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 76 Processing helix chain 'E' and resid 111 through 127 removed outlier: 3.876A pdb=" N CYS E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 167 Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 189 through 196 Processing helix chain 'E' and resid 197 through 206 Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 265 through 278 removed outlier: 4.357A pdb=" N ILE E 269 " --> pdb=" O LYS E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 304 through 310 Processing helix chain 'F' and resid 10 through 16 Processing helix chain 'F' and resid 31 through 55 removed outlier: 3.699A pdb=" N GLU F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER F 46 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER F 47 " --> pdb=" O SER F 43 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 76 Processing helix chain 'F' and resid 111 through 127 removed outlier: 3.876A pdb=" N CYS F 115 " --> pdb=" O ARG F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 167 Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 197 through 206 Processing helix chain 'F' and resid 224 through 229 Processing helix chain 'F' and resid 265 through 278 removed outlier: 4.356A pdb=" N ILE F 269 " --> pdb=" O LYS F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 304 through 310 Processing sheet with id=1, first strand: chain 'A' and resid 62 through 67 removed outlier: 6.599A pdb=" N ALA A 21 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN A 137 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE A 23 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 135 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL A 25 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.625A pdb=" N ILE A 90 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 241 through 242 Processing sheet with id=4, first strand: chain 'A' and resid 241 through 242 removed outlier: 5.177A pdb=" N PHE A 255 " --> pdb=" O HIS A 188 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 296 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A 187 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA A 294 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=6, first strand: chain 'B' and resid 62 through 67 removed outlier: 6.600A pdb=" N ALA B 21 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLN B 137 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE B 23 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B 135 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 25 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.625A pdb=" N ILE B 90 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 241 through 242 Processing sheet with id=9, first strand: chain 'B' and resid 241 through 242 removed outlier: 5.176A pdb=" N PHE B 255 " --> pdb=" O HIS B 188 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR B 296 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B 187 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA B 294 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 232 through 233 Processing sheet with id=11, first strand: chain 'C' and resid 62 through 67 removed outlier: 6.599A pdb=" N ALA C 21 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLN C 137 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE C 23 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER C 135 " --> pdb=" O PHE C 23 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 25 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.624A pdb=" N ILE C 90 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 241 through 242 Processing sheet with id=14, first strand: chain 'C' and resid 241 through 242 removed outlier: 5.176A pdb=" N PHE C 255 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR C 296 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU C 187 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA C 294 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 232 through 233 Processing sheet with id=16, first strand: chain 'D' and resid 62 through 67 removed outlier: 6.600A pdb=" N ALA D 21 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN D 137 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE D 23 " --> pdb=" O SER D 135 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER D 135 " --> pdb=" O PHE D 23 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL D 25 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 90 through 91 removed outlier: 3.625A pdb=" N ILE D 90 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 241 through 242 Processing sheet with id=19, first strand: chain 'D' and resid 241 through 242 removed outlier: 5.177A pdb=" N PHE D 255 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR D 296 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU D 187 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA D 294 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 232 through 233 Processing sheet with id=21, first strand: chain 'E' and resid 62 through 67 removed outlier: 6.599A pdb=" N ALA E 21 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN E 137 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE E 23 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER E 135 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL E 25 " --> pdb=" O VAL E 133 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 90 through 91 removed outlier: 3.625A pdb=" N ILE E 90 " --> pdb=" O ALA E 96 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 241 through 242 Processing sheet with id=24, first strand: chain 'E' and resid 241 through 242 removed outlier: 5.177A pdb=" N PHE E 255 " --> pdb=" O HIS E 188 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR E 296 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU E 187 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA E 294 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 232 through 233 Processing sheet with id=26, first strand: chain 'F' and resid 62 through 67 removed outlier: 6.599A pdb=" N ALA F 21 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN F 137 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE F 23 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER F 135 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL F 25 " --> pdb=" O VAL F 133 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'F' and resid 90 through 91 removed outlier: 3.623A pdb=" N ILE F 90 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'F' and resid 241 through 242 Processing sheet with id=29, first strand: chain 'F' and resid 241 through 242 removed outlier: 5.176A pdb=" N PHE F 255 " --> pdb=" O HIS F 188 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR F 296 " --> pdb=" O LYS F 185 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU F 187 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA F 294 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'F' and resid 232 through 233 684 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 6282 1.39 - 1.55: 8736 1.55 - 1.72: 0 1.72 - 1.88: 96 1.88 - 2.04: 24 Bond restraints: 15138 Sorted by residual: bond pdb=" CA ASP A 212 " pdb=" C ASP A 212 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.63e-02 3.76e+03 1.15e+00 bond pdb=" CA ASP D 212 " pdb=" C ASP D 212 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.63e-02 3.76e+03 1.15e+00 bond pdb=" CA ASP C 212 " pdb=" C ASP C 212 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.63e-02 3.76e+03 1.12e+00 bond pdb=" CA ASP F 212 " pdb=" C ASP F 212 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.63e-02 3.76e+03 1.12e+00 bond pdb=" CA ASP B 212 " pdb=" C ASP B 212 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.63e-02 3.76e+03 1.11e+00 ... (remaining 15133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 19652 1.08 - 2.17: 675 2.17 - 3.25: 173 3.25 - 4.33: 68 4.33 - 5.42: 42 Bond angle restraints: 20610 Sorted by residual: angle pdb=" C ARG B 55 " pdb=" CA ARG B 55 " pdb=" CB ARG B 55 " ideal model delta sigma weight residual 110.67 105.25 5.42 1.92e+00 2.71e-01 7.96e+00 angle pdb=" C ARG E 55 " pdb=" CA ARG E 55 " pdb=" CB ARG E 55 " ideal model delta sigma weight residual 110.67 105.26 5.41 1.92e+00 2.71e-01 7.94e+00 angle pdb=" C ARG C 55 " pdb=" CA ARG C 55 " pdb=" CB ARG C 55 " ideal model delta sigma weight residual 110.67 105.26 5.41 1.92e+00 2.71e-01 7.93e+00 angle pdb=" C ARG D 55 " pdb=" CA ARG D 55 " pdb=" CB ARG D 55 " ideal model delta sigma weight residual 110.67 105.27 5.40 1.92e+00 2.71e-01 7.90e+00 angle pdb=" C ARG A 55 " pdb=" CA ARG A 55 " pdb=" CB ARG A 55 " ideal model delta sigma weight residual 110.67 105.28 5.39 1.92e+00 2.71e-01 7.89e+00 ... (remaining 20605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 7945 17.82 - 35.65: 737 35.65 - 53.47: 168 53.47 - 71.30: 24 71.30 - 89.12: 30 Dihedral angle restraints: 8904 sinusoidal: 3594 harmonic: 5310 Sorted by residual: dihedral pdb=" C2A HEM F 401 " pdb=" CAA HEM F 401 " pdb=" CBA HEM F 401 " pdb=" CGA HEM F 401 " ideal model delta sinusoidal sigma weight residual -180.00 -90.88 -89.12 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C2A HEM C 401 " pdb=" CAA HEM C 401 " pdb=" CBA HEM C 401 " pdb=" CGA HEM C 401 " ideal model delta sinusoidal sigma weight residual 180.00 -90.89 -89.11 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C2A HEM B 401 " pdb=" CAA HEM B 401 " pdb=" CBA HEM B 401 " pdb=" CGA HEM B 401 " ideal model delta sinusoidal sigma weight residual -180.00 -90.90 -89.10 2 2.00e+01 2.50e-03 1.20e+01 ... (remaining 8901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1385 0.032 - 0.064: 540 0.064 - 0.096: 169 0.096 - 0.128: 108 0.128 - 0.161: 12 Chirality restraints: 2214 Sorted by residual: chirality pdb=" CB THR D 166 " pdb=" CA THR D 166 " pdb=" OG1 THR D 166 " pdb=" CG2 THR D 166 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CB THR B 166 " pdb=" CA THR B 166 " pdb=" OG1 THR B 166 " pdb=" CG2 THR B 166 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CB THR F 166 " pdb=" CA THR F 166 " pdb=" OG1 THR F 166 " pdb=" CG2 THR F 166 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 2211 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 212 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" CG ASP B 212 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP B 212 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 212 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 212 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" CG ASP E 212 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP E 212 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP E 212 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 212 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" CG ASP F 212 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP F 212 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP F 212 " 0.012 2.00e-02 2.50e+03 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 5300 2.86 - 3.37: 13370 3.37 - 3.88: 24789 3.88 - 4.39: 27576 4.39 - 4.90: 49289 Nonbonded interactions: 120324 Sorted by model distance: nonbonded pdb=" O ASP D 164 " pdb=" NH1 ARG D 264 " model vdw 2.353 3.120 nonbonded pdb=" O ASP C 164 " pdb=" NH1 ARG C 264 " model vdw 2.353 3.120 nonbonded pdb=" O ASP A 164 " pdb=" NH1 ARG A 264 " model vdw 2.353 3.120 nonbonded pdb=" O ASP E 164 " pdb=" NH1 ARG E 264 " model vdw 2.353 3.120 nonbonded pdb=" O ASP B 164 " pdb=" NH1 ARG B 264 " model vdw 2.353 3.120 ... (remaining 120319 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 0.940 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.140 Find NCS groups from input model: 0.280 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 : 0.003 0.045 15144 Z= 0.114 Angle : 0.570 5.417 20610 Z= 0.293 Chirality : 0.043 0.161 2214 Planarity : 0.004 0.046 2712 Dihedral : 15.255 89.121 5508 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.25 % Allowed : 13.76 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1854 helix: 1.09 (0.22), residues: 630 sheet: 0.63 (0.24), residues: 456 loop : -0.81 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 193 HIS 0.001 0.000 HIS E 106 PHE 0.006 0.001 PHE C 116 TYR 0.004 0.001 TYR F 223 ARG 0.003 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.11480 ( 672) hydrogen bonds : angle 5.46445 ( 1818) covalent geometry : bond 0.00286 (15138) covalent geometry : angle 0.57040 (20610) Misc. bond : bond 0.02953 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 196 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.6404 (t0) cc_final: 0.5469 (p0) REVERT: A 295 ILE cc_start: 0.8804 (pt) cc_final: 0.8546 (pt) REVERT: B 144 ASP cc_start: 0.8087 (m-30) cc_final: 0.7858 (m-30) REVERT: B 172 ASP cc_start: 0.6051 (t0) cc_final: 0.5149 (p0) REVERT: C 172 ASP cc_start: 0.6214 (t0) cc_final: 0.5348 (p0) REVERT: C 212 ASP cc_start: 0.8608 (t0) cc_final: 0.8247 (t0) REVERT: D 172 ASP cc_start: 0.6460 (t0) cc_final: 0.5475 (p0) REVERT: D 295 ILE cc_start: 0.8797 (pt) cc_final: 0.8544 (pt) REVERT: E 144 ASP cc_start: 0.8112 (m-30) cc_final: 0.7881 (m-30) REVERT: E 172 ASP cc_start: 0.6038 (t0) cc_final: 0.5142 (p0) REVERT: F 172 ASP cc_start: 0.6162 (t0) cc_final: 0.5354 (p0) REVERT: F 212 ASP cc_start: 0.8610 (t0) cc_final: 0.8250 (t0) outliers start: 4 outliers final: 0 residues processed: 200 average time/residue: 0.2799 time to fit residues: 80.7078 Evaluate side-chains 175 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 5.9990 chunk 140 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS E 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.125143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103451 restraints weight = 20510.743| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.52 r_work: 0.3094 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 15144 Z= 0.174 Angle : 0.547 4.961 20610 Z= 0.276 Chirality : 0.043 0.128 2214 Planarity : 0.004 0.034 2712 Dihedral : 8.726 85.565 2082 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.69 % Allowed : 14.27 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1854 helix: 1.38 (0.22), residues: 630 sheet: 0.63 (0.24), residues: 462 loop : -0.64 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 193 HIS 0.004 0.001 HIS C 225 PHE 0.016 0.001 PHE B 54 TYR 0.010 0.001 TYR F 186 ARG 0.002 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 672) hydrogen bonds : angle 4.76390 ( 1818) covalent geometry : bond 0.00461 (15138) covalent geometry : angle 0.54709 (20610) Misc. bond : bond 0.13837 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 1.830 Fit side-chains REVERT: A 172 ASP cc_start: 0.6659 (t0) cc_final: 0.5536 (p0) REVERT: A 173 MET cc_start: 0.7353 (tpt) cc_final: 0.7046 (tpt) REVERT: A 200 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7918 (tp40) REVERT: A 212 ASP cc_start: 0.8637 (t0) cc_final: 0.8147 (t0) REVERT: B 212 ASP cc_start: 0.8712 (t0) cc_final: 0.8437 (t0) REVERT: B 262 TYR cc_start: 0.9087 (m-80) cc_final: 0.8884 (m-80) REVERT: C 212 ASP cc_start: 0.8797 (t0) cc_final: 0.8471 (t0) REVERT: D 172 ASP cc_start: 0.6663 (t0) cc_final: 0.5528 (p0) REVERT: D 173 MET cc_start: 0.7419 (tpt) cc_final: 0.7122 (tpt) REVERT: D 200 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7951 (tp40) REVERT: D 212 ASP cc_start: 0.8631 (t0) cc_final: 0.8139 (t0) REVERT: E 212 ASP cc_start: 0.8723 (t0) cc_final: 0.8443 (t0) REVERT: E 262 TYR cc_start: 0.9088 (m-80) cc_final: 0.8881 (m-80) REVERT: F 212 ASP cc_start: 0.8806 (t0) cc_final: 0.8478 (t0) outliers start: 11 outliers final: 8 residues processed: 191 average time/residue: 0.3024 time to fit residues: 82.1080 Evaluate side-chains 153 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain F residue 134 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 43 optimal weight: 0.4980 chunk 132 optimal weight: 0.0060 chunk 124 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 chunk 167 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 overall best weight: 2.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN D 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101995 restraints weight = 20587.727| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.53 r_work: 0.3074 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.160 15144 Z= 0.170 Angle : 0.533 4.926 20610 Z= 0.267 Chirality : 0.043 0.127 2214 Planarity : 0.004 0.030 2712 Dihedral : 8.753 84.620 2082 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.59 % Allowed : 13.76 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.20), residues: 1854 helix: 1.27 (0.22), residues: 630 sheet: 0.59 (0.24), residues: 462 loop : -0.63 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 72 HIS 0.004 0.001 HIS E 225 PHE 0.019 0.002 PHE A 54 TYR 0.009 0.001 TYR F 186 ARG 0.002 0.000 ARG B 16 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 672) hydrogen bonds : angle 4.67712 ( 1818) covalent geometry : bond 0.00452 (15138) covalent geometry : angle 0.53333 (20610) Misc. bond : bond 0.15018 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.8615 (t0) cc_final: 0.8074 (t0) REVERT: B 16 ARG cc_start: 0.7723 (mmm-85) cc_final: 0.7332 (mtp-110) REVERT: B 88 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7535 (tpp80) REVERT: B 212 ASP cc_start: 0.8704 (t0) cc_final: 0.8403 (t0) REVERT: B 262 TYR cc_start: 0.9125 (m-80) cc_final: 0.8912 (m-80) REVERT: C 212 ASP cc_start: 0.8767 (t0) cc_final: 0.8429 (t0) REVERT: D 212 ASP cc_start: 0.8626 (t0) cc_final: 0.8086 (t0) REVERT: E 16 ARG cc_start: 0.7747 (mmm-85) cc_final: 0.7383 (mtp-110) REVERT: E 88 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7545 (tpp80) REVERT: E 212 ASP cc_start: 0.8717 (t0) cc_final: 0.8411 (t0) REVERT: E 262 TYR cc_start: 0.9122 (m-80) cc_final: 0.8901 (m-80) REVERT: F 212 ASP cc_start: 0.8768 (t0) cc_final: 0.8426 (t0) outliers start: 41 outliers final: 25 residues processed: 195 average time/residue: 0.3078 time to fit residues: 84.9090 Evaluate side-chains 165 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 123 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 177 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.103008 restraints weight = 20500.952| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.46 r_work: 0.3087 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 15144 Z= 0.134 Angle : 0.515 4.929 20610 Z= 0.257 Chirality : 0.042 0.126 2214 Planarity : 0.004 0.050 2712 Dihedral : 8.762 85.642 2082 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.02 % Allowed : 14.77 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1854 helix: 1.32 (0.22), residues: 630 sheet: 0.56 (0.24), residues: 462 loop : -0.60 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 193 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE B 54 TYR 0.009 0.001 TYR E 223 ARG 0.003 0.000 ARG D 16 Details of bonding type rmsd hydrogen bonds : bond 0.02927 ( 672) hydrogen bonds : angle 4.52807 ( 1818) covalent geometry : bond 0.00361 (15138) covalent geometry : angle 0.51535 (20610) Misc. bond : bond 0.12383 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.8771 (t0) cc_final: 0.8190 (t0) REVERT: B 16 ARG cc_start: 0.7725 (mmm-85) cc_final: 0.7404 (mtp-110) REVERT: B 88 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7570 (tpp80) REVERT: B 212 ASP cc_start: 0.8780 (t0) cc_final: 0.8437 (t0) REVERT: B 262 TYR cc_start: 0.9137 (m-80) cc_final: 0.8928 (m-80) REVERT: C 134 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7701 (p0) REVERT: C 212 ASP cc_start: 0.8840 (t0) cc_final: 0.8511 (t0) REVERT: D 48 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7638 (mp) REVERT: D 212 ASP cc_start: 0.8778 (t0) cc_final: 0.8199 (t0) REVERT: E 16 ARG cc_start: 0.7723 (mmm-85) cc_final: 0.7417 (mtp-110) REVERT: E 88 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7603 (tpp80) REVERT: E 212 ASP cc_start: 0.8800 (t0) cc_final: 0.8457 (t0) REVERT: E 262 TYR cc_start: 0.9154 (m-80) cc_final: 0.8941 (m-80) REVERT: F 134 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7697 (p0) REVERT: F 212 ASP cc_start: 0.8839 (t0) cc_final: 0.8516 (t0) outliers start: 32 outliers final: 25 residues processed: 197 average time/residue: 0.3202 time to fit residues: 88.1671 Evaluate side-chains 179 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 20 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.124271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.102270 restraints weight = 20630.551| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.60 r_work: 0.3089 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 15144 Z= 0.118 Angle : 0.499 4.937 20610 Z= 0.247 Chirality : 0.041 0.126 2214 Planarity : 0.003 0.027 2712 Dihedral : 8.753 86.774 2082 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.21 % Allowed : 14.46 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1854 helix: 1.35 (0.22), residues: 636 sheet: 0.59 (0.24), residues: 462 loop : -0.51 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 193 HIS 0.002 0.000 HIS B 225 PHE 0.014 0.001 PHE C 54 TYR 0.006 0.001 TYR A 186 ARG 0.002 0.000 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.02640 ( 672) hydrogen bonds : angle 4.40723 ( 1818) covalent geometry : bond 0.00322 (15138) covalent geometry : angle 0.49872 (20610) Misc. bond : bond 0.10646 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 1.665 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: A 16 ARG cc_start: 0.7504 (mtp85) cc_final: 0.7213 (mmm-85) REVERT: A 48 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7443 (mp) REVERT: A 88 ARG cc_start: 0.7719 (mtp85) cc_final: 0.7263 (mtm-85) REVERT: A 212 ASP cc_start: 0.8678 (t0) cc_final: 0.8066 (t0) REVERT: B 16 ARG cc_start: 0.7660 (mmm-85) cc_final: 0.7368 (mtp-110) REVERT: B 212 ASP cc_start: 0.8693 (t0) cc_final: 0.8330 (t0) REVERT: C 88 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7415 (mtm-85) REVERT: C 134 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7582 (p0) REVERT: C 212 ASP cc_start: 0.8736 (t0) cc_final: 0.8420 (t0) REVERT: D 88 ARG cc_start: 0.7734 (mtp85) cc_final: 0.7280 (mtm-85) REVERT: D 212 ASP cc_start: 0.8680 (t0) cc_final: 0.8074 (t0) REVERT: E 16 ARG cc_start: 0.7683 (mmm-85) cc_final: 0.7417 (mtp-110) REVERT: E 212 ASP cc_start: 0.8704 (t0) cc_final: 0.8336 (t0) REVERT: F 88 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7403 (mtm-85) REVERT: F 134 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7586 (p0) REVERT: F 212 ASP cc_start: 0.8722 (t0) cc_final: 0.8382 (t0) outliers start: 35 outliers final: 26 residues processed: 211 average time/residue: 0.3304 time to fit residues: 96.5638 Evaluate side-chains 199 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7485 > 50: distance: 23 - 47: 23.713 distance: 28 - 33: 11.967 distance: 29 - 55: 21.560 distance: 33 - 34: 21.496 distance: 33 - 39: 8.443 distance: 34 - 35: 8.541 distance: 34 - 37: 9.385 distance: 35 - 36: 25.777 distance: 35 - 40: 7.867 distance: 36 - 64: 36.091 distance: 37 - 38: 16.532 distance: 38 - 39: 20.693 distance: 40 - 41: 5.350 distance: 41 - 42: 15.142 distance: 41 - 44: 39.058 distance: 42 - 47: 18.909 distance: 44 - 45: 38.601 distance: 44 - 46: 11.306 distance: 47 - 48: 19.791 distance: 48 - 49: 8.171 distance: 48 - 51: 27.843 distance: 49 - 50: 7.531 distance: 49 - 55: 11.309 distance: 51 - 52: 20.944 distance: 52 - 53: 20.616 distance: 52 - 54: 16.906 distance: 55 - 56: 11.699 distance: 56 - 57: 30.664 distance: 56 - 59: 24.813 distance: 57 - 58: 11.859 distance: 57 - 64: 31.180 distance: 59 - 60: 31.279 distance: 60 - 61: 21.242 distance: 61 - 62: 15.135 distance: 61 - 63: 12.280 distance: 64 - 65: 15.297 distance: 65 - 66: 19.153 distance: 65 - 68: 46.632 distance: 66 - 67: 6.835 distance: 66 - 75: 16.463 distance: 68 - 69: 21.941 distance: 69 - 70: 28.892 distance: 70 - 71: 15.044 distance: 71 - 72: 17.387 distance: 72 - 73: 24.635 distance: 72 - 74: 17.417 distance: 75 - 76: 26.303 distance: 76 - 77: 21.101 distance: 76 - 79: 28.916 distance: 77 - 78: 24.941 distance: 77 - 83: 14.155 distance: 79 - 80: 14.474 distance: 80 - 81: 39.235 distance: 83 - 84: 32.474 distance: 84 - 85: 25.485 distance: 84 - 87: 27.459 distance: 85 - 86: 22.886 distance: 85 - 90: 6.387 distance: 87 - 88: 3.322 distance: 87 - 89: 16.256 distance: 90 - 91: 25.596 distance: 91 - 92: 19.089 distance: 91 - 94: 27.395 distance: 92 - 93: 8.879 distance: 92 - 101: 4.695 distance: 94 - 95: 18.511 distance: 95 - 96: 35.309 distance: 96 - 97: 6.475 distance: 97 - 98: 13.944 distance: 98 - 99: 29.247 distance: 98 - 100: 24.320 distance: 101 - 102: 12.710 distance: 101 - 147: 27.191 distance: 102 - 103: 12.230 distance: 102 - 105: 34.441 distance: 103 - 104: 15.802 distance: 103 - 106: 20.038 distance: 104 - 144: 29.452 distance: 106 - 107: 18.140 distance: 107 - 108: 38.663 distance: 107 - 110: 18.130 distance: 108 - 109: 20.770 distance: 108 - 111: 21.822