Starting phenix.real_space_refine on Wed May 14 20:00:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5a6e_3062/05_2025/5a6e_3062_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a6e_3062/05_2025/5a6e_3062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5a6e_3062/05_2025/5a6e_3062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a6e_3062/05_2025/5a6e_3062.map" model { file = "/net/cci-nas-00/data/ceres_data/5a6e_3062/05_2025/5a6e_3062_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a6e_3062/05_2025/5a6e_3062_trim.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 S 43 5.16 5 C 3823 2.51 5 N 1024 2.21 5 O 1101 1.98 5 H 5102 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "C ARG 438": not complete - not flipped Residue "C ARG 438": not complete - not flipped Residue "C ARG 443": not complete - not flipped Residue "C ARG 443": not complete - not flipped Residue "C ARG 534": not complete - not flipped Residue "C ARG 534": not complete - not flipped Residue "C ARG 578": not complete - not flipped Residue "C ARG 578": not complete - not flipped Residue "C ARG 579": not complete - not flipped Residue "C ARG 579": not complete - not flipped Residue "C ARG 592": not complete - not flipped Residue "C ARG 592": not complete - not flipped Residue "C ARG 883": not complete - not flipped Residue "C ARG 883": not complete - not flipped Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11093 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 695 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'TRANS': 138} Chain breaks: 4 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 139 Planarities with less than four sites: {'UNK:plan-1': 139} Unresolved non-hydrogen planarities: 139 Chain: "B" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1516 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "C" Number of atoms: 8667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 8653 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 23, 'TRANS': 516} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 540, 8653 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 23, 'TRANS': 516} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 8731 Chain: "D" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 215 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'CIS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'UNK:plan-1': 43} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 9.39, per 1000 atoms: 0.85 Number of scatterers: 11093 At special positions: 0 Unit cell: (83.2, 108.16, 132.08, 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) S 43 16.00 O 1101 8.00 N 1024 7.00 C 3823 6.00 H 5102 1.00 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: 2.77 Conformation dependent library (CDL) restraints added in 879.7 milliseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 71.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.547A pdb=" N UNK A 74 " --> pdb=" O UNK A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 116 removed outlier: 3.694A pdb=" N UNK A 93 " --> pdb=" O UNK A 89 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N UNK A 116 " --> pdb=" O UNK A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 137 removed outlier: 3.918A pdb=" N UNK A 125 " --> pdb=" O UNK A 121 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N UNK A 137 " --> pdb=" O UNK A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 167 removed outlier: 3.672A pdb=" N UNK A 152 " --> pdb=" O UNK A 148 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 179 through 199 removed outlier: 4.072A pdb=" N UNK A 183 " --> pdb=" O UNK A 179 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N UNK A 185 " --> pdb=" O UNK A 181 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N UNK A 196 " --> pdb=" O UNK A 192 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N UNK A 199 " --> pdb=" O UNK A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 234 removed outlier: 3.572A pdb=" N UNK A 216 " --> pdb=" O UNK A 212 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N UNK A 217 " --> pdb=" O UNK A 213 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK A 218 " --> pdb=" O UNK A 214 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N UNK A 234 " --> pdb=" O UNK A 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 276 removed outlier: 4.000A pdb=" N HIS B 270 " --> pdb=" O CYS B 266 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 273 " --> pdb=" O GLN B 269 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA B 274 " --> pdb=" O HIS B 270 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 292 Processing helix chain 'B' and resid 303 through 337 removed outlier: 3.554A pdb=" N GLN B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU B 308 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Proline residue: B 322 - end of helix Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.566A pdb=" N LEU C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 removed outlier: 3.674A pdb=" N VAL C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 394 through 399' Processing helix chain 'C' and resid 417 through 424 removed outlier: 3.879A pdb=" N LEU C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 461 removed outlier: 4.059A pdb=" N ALA C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP C 447 " --> pdb=" O ARG C 443 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 removed outlier: 3.894A pdb=" N PHE C 477 " --> pdb=" O GLU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 499 Processing helix chain 'C' and resid 504 through 513 removed outlier: 3.572A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 509 " --> pdb=" O THR C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 535 removed outlier: 3.529A pdb=" N CYS C 535 " --> pdb=" O MET C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 567 removed outlier: 3.950A pdb=" N ALA C 562 " --> pdb=" O SER C 558 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA C 563 " --> pdb=" O PHE C 559 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 564 " --> pdb=" O THR C 560 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS C 565 " --> pdb=" O TYR C 561 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS C 567 " --> pdb=" O ALA C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 792 removed outlier: 4.143A pdb=" N TYR C 788 " --> pdb=" O GLY C 784 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN C 789 " --> pdb=" O ASN C 785 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 792 " --> pdb=" O TYR C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.806A pdb=" N LEU C 820 " --> pdb=" O GLU C 816 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 821 " --> pdb=" O HIS C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 838 through 844 Processing helix chain 'C' and resid 867 through 870 Processing helix chain 'C' and resid 871 through 885 removed outlier: 3.689A pdb=" N ILE C 875 " --> pdb=" O ASP C 871 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN C 877 " --> pdb=" O LYS C 873 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C 880 " --> pdb=" O VAL C 876 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N MET C 881 " --> pdb=" O ASN C 877 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 882 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 883 " --> pdb=" O GLN C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 903 removed outlier: 4.402A pdb=" N ARG C 901 " --> pdb=" O SER C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 924 removed outlier: 4.603A pdb=" N SER C 916 " --> pdb=" O SER C 912 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS C 917 " --> pdb=" O LEU C 913 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 918 " --> pdb=" O ALA C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 934 through 939 Processing helix chain 'C' and resid 945 through 956 removed outlier: 3.784A pdb=" N ASP C 949 " --> pdb=" O ILE C 945 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR C 950 " --> pdb=" O SER C 946 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU C 951 " --> pdb=" O MET C 947 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 953 " --> pdb=" O ASP C 949 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 970 removed outlier: 3.569A pdb=" N ILE C 964 " --> pdb=" O TYR C 960 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR C 965 " --> pdb=" O MET C 961 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 966 " --> pdb=" O ILE C 962 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 967 " --> pdb=" O THR C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 992 Processing helix chain 'C' and resid 995 through 1003 removed outlier: 3.641A pdb=" N LYS C1001 " --> pdb=" O ARG C 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1098 removed outlier: 3.764A pdb=" N UNK D1088 " --> pdb=" O UNK D1084 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N UNK D1097 " --> pdb=" O UNK D1093 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1113 removed outlier: 3.655A pdb=" N UNK D1110 " --> pdb=" O UNK D1106 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N UNK D1111 " --> pdb=" O UNK D1107 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N UNK D1112 " --> pdb=" O UNK D1108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N UNK D1113 " --> pdb=" O UNK D1109 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 408 through 412 removed outlier: 3.598A pdb=" N CYS C 387 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA C 431 " --> pdb=" O HIS C 352 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 467 through 470 removed outlier: 3.589A pdb=" N VAL C 468 " --> pdb=" O HIS C 484 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.664A pdb=" N TYR C 603 " --> pdb=" O TYR C 541 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS C 573 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing sheet with id=CD, first strand: chain 'C' and resid 829 through 833 removed outlier: 3.711A pdb=" N LEU C 811 " --> pdb=" O MET C 832 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 780 " --> pdb=" O LEU C 810 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 777 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 855 " --> pdb=" O ILE C 891 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU C 893 " --> pdb=" O VAL C 855 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 894 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing sheet with id=CE, first strand: chain 'C' and resid 979 through 984 removed outlier: 3.637A pdb=" N VAL C1162 " --> pdb=" O MET C 983 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C1009 " --> pdb=" O ILE C1165 " (cutoff:3.500A) Processing sheet with id=CF, first strand: chain 'C' and resid 1012 through 1013 removed outlier: 3.749A pdb=" N LEU C1147 " --> pdb=" O ILE C1013 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 822 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: 3.44 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.28: 6087 1.28 - 1.73: 5030 1.73 - 2.18: 65 2.18 - 2.63: 7 2.63 - 3.07: 7 Bond restraints: 11196 Sorted by residual: bond pdb=" NH2 ARG C 883 " pdb="HH21BARG C 883 " ideal model delta sigma weight residual 0.860 3.073 -2.213 2.00e-02 2.50e+03 1.22e+04 bond pdb=" NH2 ARG C 579 " pdb="HH21BARG C 579 " ideal model delta sigma weight residual 0.860 3.070 -2.210 2.00e-02 2.50e+03 1.22e+04 bond pdb=" NH2 ARG C 438 " pdb="HH21BARG C 438 " ideal model delta sigma weight residual 0.860 3.070 -2.210 2.00e-02 2.50e+03 1.22e+04 bond pdb=" NH2 ARG C 592 " pdb="HH21BARG C 592 " ideal model delta sigma weight residual 0.860 3.070 -2.210 2.00e-02 2.50e+03 1.22e+04 bond pdb=" NH2 ARG C 578 " pdb="HH21BARG C 578 " ideal model delta sigma weight residual 0.860 3.068 -2.208 2.00e-02 2.50e+03 1.22e+04 ... (remaining 11191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 23.86: 19835 23.86 - 47.72: 0 47.72 - 71.58: 7 71.58 - 95.44: 7 95.44 - 119.30: 14 Bond angle restraints: 19863 Sorted by residual: angle pdb=" NH1 ARG C 443 " pdb=" CZ ARG C 443 " pdb=" NH2 ARG C 443 " ideal model delta sigma weight residual 119.30 0.00 119.30 1.30e+00 5.92e-01 8.42e+03 angle pdb=" NH1 ARG C 534 " pdb=" CZ ARG C 534 " pdb=" NH2 ARG C 534 " ideal model delta sigma weight residual 119.30 0.00 119.30 1.30e+00 5.92e-01 8.42e+03 angle pdb=" NH1 ARG C 579 " pdb=" CZ ARG C 579 " pdb=" NH2 ARG C 579 " ideal model delta sigma weight residual 119.30 0.00 119.30 1.30e+00 5.92e-01 8.42e+03 angle pdb=" NH1 ARG C 883 " pdb=" CZ ARG C 883 " pdb=" NH2 ARG C 883 " ideal model delta sigma weight residual 119.30 0.00 119.30 1.30e+00 5.92e-01 8.42e+03 angle pdb=" NH1 ARG C 592 " pdb=" CZ ARG C 592 " pdb=" NH2 ARG C 592 " ideal model delta sigma weight residual 119.30 0.00 119.30 1.30e+00 5.92e-01 8.42e+03 ... (remaining 19858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 5222 35.98 - 71.97: 159 71.97 - 107.95: 1 107.95 - 143.93: 0 143.93 - 179.91: 7 Dihedral angle restraints: 5389 sinusoidal: 2620 harmonic: 2769 Sorted by residual: dihedral pdb=" CD ARG C 592 " pdb=" NE ARG C 592 " pdb=" CZ ARG C 592 " pdb=" NH1 ARG C 592 " ideal model delta sinusoidal sigma weight residual 0.00 -179.91 179.91 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG C 883 " pdb=" NE ARG C 883 " pdb=" CZ ARG C 883 " pdb=" NH1 ARG C 883 " ideal model delta sinusoidal sigma weight residual 0.00 179.88 -179.88 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG C 534 " pdb=" NE ARG C 534 " pdb=" CZ ARG C 534 " pdb=" NH1 ARG C 534 " ideal model delta sinusoidal sigma weight residual 0.00 179.86 -179.86 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 5386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 612 0.036 - 0.072: 241 0.072 - 0.108: 94 0.108 - 0.145: 26 0.145 - 0.181: 10 Chirality restraints: 983 Sorted by residual: chirality pdb=" CA ASN C 785 " pdb=" N ASN C 785 " pdb=" C ASN C 785 " pdb=" CB ASN C 785 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA MET C 828 " pdb=" N MET C 828 " pdb=" C MET C 828 " pdb=" CB MET C 828 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ILE C1013 " pdb=" N ILE C1013 " pdb=" C ILE C1013 " pdb=" CB ILE C1013 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.72e-01 ... (remaining 980 not shown) Planarity restraints: 1669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 499 " -0.162 2.00e-02 2.50e+03 1.83e-01 5.00e+02 pdb=" CG ASN C 499 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN C 499 " 0.156 2.00e-02 2.50e+03 pdb=" ND2 ASN C 499 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 499 " 0.269 2.00e-02 2.50e+03 pdb="HD22 ASN C 499 " -0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 529 " 0.147 2.00e-02 2.50e+03 1.65e-01 4.10e+02 pdb=" CD GLN C 529 " -0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN C 529 " -0.144 2.00e-02 2.50e+03 pdb=" NE2 GLN C 529 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN C 529 " -0.246 2.00e-02 2.50e+03 pdb="HE22 GLN C 529 " 0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 336 " -0.143 2.00e-02 2.50e+03 1.60e-01 3.83e+02 pdb=" CD GLN B 336 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN B 336 " 0.138 2.00e-02 2.50e+03 pdb=" NE2 GLN B 336 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 336 " 0.235 2.00e-02 2.50e+03 pdb="HE22 GLN B 336 " -0.241 2.00e-02 2.50e+03 ... (remaining 1666 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.61: 16 1.61 - 2.36: 3638 2.36 - 3.10: 31127 3.10 - 3.85: 38142 3.85 - 4.60: 62965 Warning: very small nonbonded interaction distances. Nonbonded interactions: 135888 Sorted by model distance: nonbonded pdb=" NH1 ARG C 883 " pdb="HH22AARG C 883 " model vdw 0.860 2.080 nonbonded pdb=" NH1 ARG C 534 " pdb="HH21AARG C 534 " model vdw 0.860 2.080 nonbonded pdb=" NH1 ARG C 443 " pdb="HH22AARG C 443 " model vdw 0.860 2.080 nonbonded pdb=" NH1 ARG C 579 " pdb="HH22AARG C 579 " model vdw 0.860 2.080 nonbonded pdb=" NH1 ARG C 438 " pdb="HH22AARG C 438 " model vdw 0.860 2.080 ... (remaining 135883 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.240 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.300 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 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 : 0.010 0.090 6094 Z= 0.640 Angle : 3.735 119.300 8281 Z= 2.818 Chirality : 0.048 0.181 983 Planarity : 0.006 0.073 1066 Dihedral : 15.551 179.913 2097 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.06 % Favored : 88.78 % Rotamer: Outliers : 3.19 % Allowed : 7.61 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -5.00 (0.24), residues: 624 helix: -4.12 (0.19), residues: 212 sheet: -1.55 (0.48), residues: 85 loop : -3.29 (0.26), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 528 HIS 0.010 0.002 HIS C 478 PHE 0.018 0.002 PHE C 564 TYR 0.033 0.003 TYR C 788 ARG 0.004 0.000 ARG C 901 Details of bonding type rmsd hydrogen bonds : bond 0.21444 ( 286) hydrogen bonds : angle 9.21519 ( 822) covalent geometry : bond 0.01049 ( 6094) covalent geometry : angle 3.73482 ( 8281) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 244 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.801 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 PHE cc_start: 0.7535 (m-80) cc_final: 0.6971 (m-10) REVERT: C 499 ASN cc_start: 0.9666 (OUTLIER) cc_final: 0.9311 (m-40) REVERT: C 531 MET cc_start: 0.9759 (ttm) cc_final: 0.9518 (tpp) REVERT: C 932 MET cc_start: 0.9166 (ttp) cc_final: 0.8761 (ttp) outliers start: 18 outliers final: 5 residues processed: 101 average time/residue: 0.3066 time to fit residues: 41.9737 Evaluate side-chains 64 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.046764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.036029 restraints weight = 272666.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.037636 restraints weight = 112710.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.038826 restraints weight = 62563.882| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6094 Z= 0.168 Angle : 0.729 8.069 8281 Z= 0.386 Chirality : 0.039 0.152 983 Planarity : 0.006 0.054 1066 Dihedral : 16.877 177.715 867 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.27), residues: 624 helix: -2.71 (0.26), residues: 230 sheet: -1.26 (0.51), residues: 90 loop : -2.68 (0.29), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 304 HIS 0.005 0.001 HIS C 567 PHE 0.020 0.002 PHE C 368 TYR 0.012 0.002 TYR C 797 ARG 0.014 0.001 ARG C 795 Details of bonding type rmsd hydrogen bonds : bond 0.06381 ( 286) hydrogen bonds : angle 6.10946 ( 822) covalent geometry : bond 0.00341 ( 6094) covalent geometry : angle 0.72900 ( 8281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 244 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.763 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9330 (mtp) cc_final: 0.9095 (tmm) REVERT: C 932 MET cc_start: 0.8730 (ttp) cc_final: 0.8339 (ttp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.3609 time to fit residues: 31.7129 Evaluate side-chains 56 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 57.187 > 50: distance: 51 - 63: 6.615 distance: 63 - 64: 8.363 distance: 63 - 69: 23.341 distance: 64 - 65: 10.989 distance: 64 - 67: 10.816 distance: 64 - 70: 12.656 distance: 65 - 66: 16.820 distance: 65 - 74: 28.318 distance: 67 - 68: 9.746 distance: 67 - 71: 6.501 distance: 67 - 72: 13.841 distance: 68 - 73: 12.064 distance: 74 - 75: 19.263 distance: 74 - 81: 16.818 distance: 75 - 76: 16.620 distance: 75 - 78: 14.998 distance: 75 - 82: 13.588 distance: 76 - 77: 32.203 distance: 76 - 90: 19.444 distance: 78 - 79: 15.106 distance: 78 - 80: 12.696 distance: 78 - 83: 19.363 distance: 79 - 84: 7.011 distance: 79 - 85: 14.231 distance: 79 - 86: 6.731 distance: 80 - 87: 6.832 distance: 80 - 88: 6.081 distance: 80 - 89: 11.355 distance: 90 - 91: 14.222 distance: 90 - 96: 15.012 distance: 91 - 92: 31.569 distance: 91 - 94: 33.324 distance: 91 - 97: 30.544 distance: 92 - 93: 26.844 distance: 92 - 101: 13.421 distance: 94 - 95: 18.315 distance: 94 - 98: 33.285 distance: 94 - 99: 19.697 distance: 95 - 100: 18.679 distance: 101 - 102: 17.461 distance: 101 - 107: 7.739 distance: 102 - 103: 23.032 distance: 102 - 105: 25.196 distance: 102 - 108: 7.211 distance: 103 - 104: 15.465 distance: 103 - 115: 16.709 distance: 105 - 106: 12.366 distance: 105 - 109: 11.293 distance: 105 - 110: 9.099 distance: 106 - 107: 6.242 distance: 106 - 111: 5.389 distance: 106 - 112: 6.998 distance: 107 - 113: 7.068 distance: 107 - 114: 4.870 distance: 115 - 116: 13.280 distance: 115 - 120: 18.226 distance: 116 - 117: 11.574 distance: 116 - 119: 14.824 distance: 116 - 121: 14.631 distance: 117 - 118: 19.702 distance: 117 - 125: 14.689 distance: 119 - 122: 3.756 distance: 119 - 123: 4.734 distance: 119 - 124: 7.743 distance: 125 - 126: 11.756 distance: 125 - 132: 19.617 distance: 126 - 127: 17.934 distance: 126 - 129: 3.743 distance: 126 - 133: 5.807 distance: 127 - 128: 16.704 distance: 127 - 139: 21.841 distance: 129 - 130: 10.499 distance: 129 - 131: 9.961 distance: 129 - 134: 8.457 distance: 130 - 135: 5.174 distance: 131 - 136: 3.501 distance: 131 - 138: 5.011 distance: 139 - 140: 5.783 distance: 139 - 145: 29.494 distance: 140 - 141: 17.597 distance: 140 - 143: 4.327 distance: 140 - 146: 12.237 distance: 141 - 142: 13.349 distance: 141 - 150: 10.647 distance: 142 - 202: 15.376 distance: 143 - 147: 9.012 distance: 143 - 148: 5.260 distance: 144 - 149: 16.746 distance: 150 - 151: 11.656 distance: 150 - 157: 24.070 distance: 151 - 152: 7.630 distance: 151 - 154: 7.300 distance: 151 - 158: 4.481 distance: 152 - 153: 7.595 distance: 152 - 164: 5.200 distance: 153 - 216: 8.933 distance: 154 - 155: 4.937 distance: 154 - 156: 3.594 distance: 154 - 159: 6.348 distance: 155 - 160: 7.598 distance: 156 - 163: 3.334 distance: 164 - 165: 5.499 distance: 164 - 172: 21.261 distance: 165 - 166: 7.706 distance: 165 - 168: 6.465 distance: 165 - 173: 4.342 distance: 166 - 167: 8.016 distance: 166 - 183: 4.740 distance: 167 - 232: 9.993 distance: 168 - 169: 5.886 distance: 168 - 174: 3.890 distance: 168 - 175: 6.924 distance: 169 - 170: 3.319 distance: 183 - 191: 4.552 distance: 184 - 185: 3.222 distance: 184 - 187: 6.295 distance: 184 - 192: 3.530 distance: 185 - 186: 4.263 distance: 185 - 202: 3.156 distance: 186 - 250: 9.046 distance: 187 - 188: 6.782 distance: 187 - 189: 3.927 distance: 190 - 199: 5.291 distance: 190 - 200: 3.011 distance: 190 - 201: 5.422