Starting phenix.real_space_refine on Sat May 10 04:49:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r1u_18828/05_2025/8r1u_18828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r1u_18828/05_2025/8r1u_18828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r1u_18828/05_2025/8r1u_18828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r1u_18828/05_2025/8r1u_18828.map" model { file = "/net/cci-nas-00/data/ceres_data/8r1u_18828/05_2025/8r1u_18828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r1u_18828/05_2025/8r1u_18828.cif" } resolution = 3.19 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= 0.002 sd= 0.013 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 Ca 2 9.91 5 S 64 5.16 5 C 3154 2.51 5 N 846 2.21 5 O 966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5032 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2515 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 21, 'TRANS': 307} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 4.34, per 1000 atoms: 0.86 Number of scatterers: 5032 At special positions: 0 Unit cell: (92.2019, 101.681, 74.1062, 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) Ca 2 19.99 S 64 16.00 O 966 8.00 N 846 7.00 C 3154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 903 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A1071 " distance=2.03 Simple disulfide: pdb=" SG CYS A 934 " - pdb=" SG CYS A1033 " distance=2.03 Simple disulfide: pdb=" SG CYS A 953 " - pdb=" SG CYS A 960 " distance=2.03 Simple disulfide: pdb=" SG CYS A1081 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1095 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1146 " distance=2.03 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1134 " distance=2.04 Simple disulfide: pdb=" SG CYS A1136 " - pdb=" SG CYS A1161 " distance=2.03 Simple disulfide: pdb=" SG CYS A1152 " - pdb=" SG CYS A1181 " distance=2.03 Simple disulfide: pdb=" SG CYS A1165 " - pdb=" SG CYS A1206 " distance=2.03 Simple disulfide: pdb=" SG CYS A1174 " - pdb=" SG CYS B1174 " distance=2.03 Simple disulfide: pdb=" SG CYS A1185 " - pdb=" SG CYS A1196 " distance=2.03 Simple disulfide: pdb=" SG CYS A1189 " - pdb=" SG CYS A1228 " distance=2.03 Simple disulfide: pdb=" SG CYS A1210 " - pdb=" SG CYS A1224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 903 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B1071 " distance=2.03 Simple disulfide: pdb=" SG CYS B 934 " - pdb=" SG CYS B1033 " distance=2.03 Simple disulfide: pdb=" SG CYS B 953 " - pdb=" SG CYS B 960 " distance=2.03 Simple disulfide: pdb=" SG CYS B1081 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1095 " - pdb=" SG CYS B1119 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1146 " distance=2.03 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1134 " distance=2.04 Simple disulfide: pdb=" SG CYS B1136 " - pdb=" SG CYS B1161 " distance=2.03 Simple disulfide: pdb=" SG CYS B1152 " - pdb=" SG CYS B1181 " distance=2.03 Simple disulfide: pdb=" SG CYS B1165 " - pdb=" SG CYS B1206 " distance=2.03 Simple disulfide: pdb=" SG CYS B1185 " - pdb=" SG CYS B1196 " distance=2.03 Simple disulfide: pdb=" SG CYS B1189 " - pdb=" SG CYS B1228 " distance=2.03 Simple disulfide: pdb=" SG CYS B1210 " - pdb=" SG CYS B1224 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 604.5 milliseconds 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1204 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 6 sheets defined 22.8% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 1026 through 1029 Processing helix chain 'A' and resid 1058 through 1064 Processing helix chain 'A' and resid 1079 through 1084 Processing helix chain 'A' and resid 1087 through 1096 Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1103 through 1108 removed outlier: 3.883A pdb=" N ALA A1108 " --> pdb=" O ALA A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1126 Processing helix chain 'A' and resid 1130 through 1150 removed outlier: 3.991A pdb=" N ALA A1138 " --> pdb=" O CYS A1134 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A1142 " --> pdb=" O ALA A1138 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A1149 " --> pdb=" O ALA A1145 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A1150 " --> pdb=" O CYS A1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1029 Processing helix chain 'B' and resid 1058 through 1064 Processing helix chain 'B' and resid 1079 through 1084 Processing helix chain 'B' and resid 1087 through 1096 Processing helix chain 'B' and resid 1097 through 1099 No H-bonds generated for 'chain 'B' and resid 1097 through 1099' Processing helix chain 'B' and resid 1100 through 1102 No H-bonds generated for 'chain 'B' and resid 1100 through 1102' Processing helix chain 'B' and resid 1103 through 1108 removed outlier: 3.882A pdb=" N ALA B1108 " --> pdb=" O ALA B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1126 Processing helix chain 'B' and resid 1130 through 1150 removed outlier: 3.991A pdb=" N ALA B1138 " --> pdb=" O CYS B1134 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B1142 " --> pdb=" O ALA B1138 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B1149 " --> pdb=" O ALA B1145 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B1150 " --> pdb=" O CYS B1146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 918 through 920 removed outlier: 3.511A pdb=" N TYR A 911 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1011 " --> pdb=" O ASN A1023 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP A1014 " --> pdb=" O LEU A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 979 through 982 removed outlier: 5.842A pdb=" N SER A 961 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 951 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 963 " --> pdb=" O GLU A 949 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A 944 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLN A 931 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 946 " --> pdb=" O LEU A 929 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1176 through 1178 Processing sheet with id=AA4, first strand: chain 'B' and resid 918 through 920 removed outlier: 3.512A pdb=" N TYR B 911 " --> pdb=" O TYR B 919 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B1011 " --> pdb=" O ASN B1023 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP B1014 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 979 through 982 removed outlier: 5.841A pdb=" N SER B 961 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 951 " --> pdb=" O SER B 961 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B 963 " --> pdb=" O GLU B 949 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE B 944 " --> pdb=" O GLN B 931 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLN B 931 " --> pdb=" O PHE B 944 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B 946 " --> pdb=" O LEU B 929 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1176 through 1178 152 hydrogen bonds defined for protein. 414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1666 1.35 - 1.46: 1239 1.46 - 1.58: 2193 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 5166 Sorted by residual: bond pdb=" CA CYS A1161 " pdb=" CB CYS A1161 " ideal model delta sigma weight residual 1.522 1.531 -0.009 7.00e-03 2.04e+04 1.62e+00 bond pdb=" CA CYS B1161 " pdb=" CB CYS B1161 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.40e+00 bond pdb=" CA CYS B1161 " pdb=" C CYS B1161 " ideal model delta sigma weight residual 1.531 1.524 0.007 7.40e-03 1.83e+04 9.79e-01 bond pdb=" CA CYS A1161 " pdb=" C CYS A1161 " ideal model delta sigma weight residual 1.531 1.524 0.007 7.40e-03 1.83e+04 9.13e-01 bond pdb=" N GLY B 954 " pdb=" CA GLY B 954 " ideal model delta sigma weight residual 1.444 1.455 -0.011 1.32e-02 5.74e+03 7.13e-01 ... (remaining 5161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 6816 1.06 - 2.12: 156 2.12 - 3.18: 54 3.18 - 4.24: 6 4.24 - 5.30: 4 Bond angle restraints: 7036 Sorted by residual: angle pdb=" C ASP B1015 " pdb=" N LYS B1016 " pdb=" CA LYS B1016 " ideal model delta sigma weight residual 121.54 126.84 -5.30 1.91e+00 2.74e-01 7.70e+00 angle pdb=" C ASP A1015 " pdb=" N LYS A1016 " pdb=" CA LYS A1016 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.55e+00 angle pdb=" C SER A 939 " pdb=" N THR A 940 " pdb=" CA THR A 940 " ideal model delta sigma weight residual 122.46 125.30 -2.84 1.41e+00 5.03e-01 4.06e+00 angle pdb=" C SER B 939 " pdb=" N THR B 940 " pdb=" CA THR B 940 " ideal model delta sigma weight residual 122.46 125.26 -2.80 1.41e+00 5.03e-01 3.93e+00 angle pdb=" N PRO A1215 " pdb=" CA PRO A1215 " pdb=" C PRO A1215 " ideal model delta sigma weight residual 114.92 112.81 2.11 1.19e+00 7.06e-01 3.16e+00 ... (remaining 7031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 2738 16.23 - 32.47: 285 32.47 - 48.70: 76 48.70 - 64.93: 18 64.93 - 81.17: 12 Dihedral angle restraints: 3129 sinusoidal: 1243 harmonic: 1886 Sorted by residual: dihedral pdb=" CB CYS A1106 " pdb=" SG CYS A1106 " pdb=" SG CYS A1146 " pdb=" CB CYS A1146 " ideal model delta sinusoidal sigma weight residual -86.00 -166.05 80.05 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS B1106 " pdb=" SG CYS B1106 " pdb=" SG CYS B1146 " pdb=" CB CYS B1146 " ideal model delta sinusoidal sigma weight residual -86.00 -166.03 80.03 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS B 953 " pdb=" SG CYS B 953 " pdb=" SG CYS B 960 " pdb=" CB CYS B 960 " ideal model delta sinusoidal sigma weight residual -86.00 -159.20 73.20 1 1.00e+01 1.00e-02 6.83e+01 ... (remaining 3126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 413 0.024 - 0.049: 194 0.049 - 0.073: 54 0.073 - 0.097: 49 0.097 - 0.121: 44 Chirality restraints: 754 Sorted by residual: chirality pdb=" CG LEU B1203 " pdb=" CB LEU B1203 " pdb=" CD1 LEU B1203 " pdb=" CD2 LEU B1203 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CG LEU A1203 " pdb=" CB LEU A1203 " pdb=" CD1 LEU A1203 " pdb=" CD2 LEU A1203 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA LYS A1016 " pdb=" N LYS A1016 " pdb=" C LYS A1016 " pdb=" CB LYS A1016 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 751 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A1157 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO A1158 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B1157 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO B1158 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B1158 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B1158 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B1025 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO B1026 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B1026 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B1026 " 0.014 5.00e-02 4.00e+02 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 836 2.76 - 3.30: 4701 3.30 - 3.83: 8342 3.83 - 4.37: 9045 4.37 - 4.90: 15462 Nonbonded interactions: 38386 Sorted by model distance: nonbonded pdb=" OG SER A1025 " pdb=" OE1 GLU A1027 " model vdw 2.230 3.040 nonbonded pdb=" OG SER B1025 " pdb=" OE1 GLU B1027 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASN B1045 " pdb="CA CA B1401 " model vdw 2.277 2.510 nonbonded pdb=" OD1 ASN A1045 " pdb="CA CA A1401 " model vdw 2.277 2.510 nonbonded pdb=" OD2 ASP B1079 " pdb=" OG1 THR B1082 " model vdw 2.287 3.040 ... (remaining 38381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.960 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.530 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.002 0.019 5195 Z= 0.107 Angle : 0.458 5.301 7094 Z= 0.242 Chirality : 0.042 0.121 754 Planarity : 0.003 0.029 930 Dihedral : 14.256 81.168 1838 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 18.71 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.33), residues: 654 helix: 0.59 (0.48), residues: 128 sheet: 1.80 (0.77), residues: 52 loop : -1.20 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B1201 HIS 0.001 0.000 HIS B1107 PHE 0.005 0.001 PHE B1135 TYR 0.004 0.001 TYR B1116 ARG 0.001 0.000 ARG A1198 Details of bonding type rmsd hydrogen bonds : bond 0.18048 ( 152) hydrogen bonds : angle 7.39812 ( 414) SS BOND : bond 0.00176 ( 29) SS BOND : angle 0.49112 ( 58) covalent geometry : bond 0.00212 ( 5166) covalent geometry : angle 0.45755 ( 7036) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1122 ASP cc_start: 0.8302 (t0) cc_final: 0.7984 (t70) REVERT: B 1122 ASP cc_start: 0.8299 (t0) cc_final: 0.7982 (t0) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.3459 time to fit residues: 11.7963 Evaluate side-chains 15 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 0.0970 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 HIS ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 HIS ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 HIS ** B1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.079136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.058857 restraints weight = 18577.816| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 5.62 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5195 Z= 0.099 Angle : 0.488 5.780 7094 Z= 0.258 Chirality : 0.044 0.129 754 Planarity : 0.003 0.032 930 Dihedral : 2.904 9.892 706 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.72 % Allowed : 17.09 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.32), residues: 654 helix: 0.40 (0.46), residues: 128 sheet: 2.10 (0.74), residues: 52 loop : -1.34 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1014 HIS 0.004 0.001 HIS A1107 PHE 0.005 0.001 PHE B1135 TYR 0.005 0.001 TYR A 906 ARG 0.001 0.000 ARG A1198 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 152) hydrogen bonds : angle 5.71982 ( 414) SS BOND : bond 0.00182 ( 29) SS BOND : angle 0.51475 ( 58) covalent geometry : bond 0.00214 ( 5166) covalent geometry : angle 0.48739 ( 7036) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1106 CYS cc_start: 0.7413 (m) cc_final: 0.6599 (t) REVERT: A 1122 ASP cc_start: 0.8343 (t0) cc_final: 0.7986 (t0) REVERT: B 1106 CYS cc_start: 0.7368 (m) cc_final: 0.6559 (t) REVERT: B 1122 ASP cc_start: 0.8319 (t0) cc_final: 0.7973 (t0) outliers start: 4 outliers final: 4 residues processed: 21 average time/residue: 0.3212 time to fit residues: 8.5534 Evaluate side-chains 23 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1011 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 5 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 47 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.075060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.054700 restraints weight = 19561.446| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 5.69 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 5195 Z= 0.285 Angle : 0.589 5.785 7094 Z= 0.318 Chirality : 0.046 0.130 754 Planarity : 0.004 0.033 930 Dihedral : 3.733 14.203 706 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.08 % Allowed : 19.78 % Favored : 79.14 % 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: -1.16 (0.32), residues: 654 helix: -0.30 (0.43), residues: 140 sheet: 1.07 (0.63), residues: 80 loop : -1.37 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B1155 HIS 0.008 0.002 HIS B1107 PHE 0.012 0.002 PHE B1164 TYR 0.015 0.002 TYR B1116 ARG 0.002 0.000 ARG A1198 Details of bonding type rmsd hydrogen bonds : bond 0.05512 ( 152) hydrogen bonds : angle 5.73072 ( 414) SS BOND : bond 0.00372 ( 29) SS BOND : angle 0.71905 ( 58) covalent geometry : bond 0.00623 ( 5166) covalent geometry : angle 0.58789 ( 7036) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1122 ASP cc_start: 0.8281 (t0) cc_final: 0.7937 (t0) REVERT: B 1122 ASP cc_start: 0.8329 (t0) cc_final: 0.7980 (t0) outliers start: 6 outliers final: 4 residues processed: 20 average time/residue: 0.4077 time to fit residues: 10.1558 Evaluate side-chains 18 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1011 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1107 HIS ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1107 HIS ** B1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.078339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.057730 restraints weight = 19092.494| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 5.80 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5195 Z= 0.094 Angle : 0.456 4.421 7094 Z= 0.242 Chirality : 0.044 0.126 754 Planarity : 0.003 0.035 930 Dihedral : 3.235 10.994 706 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.08 % Allowed : 18.53 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.33), residues: 654 helix: 0.35 (0.48), residues: 130 sheet: 1.39 (0.63), residues: 80 loop : -1.24 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1014 HIS 0.004 0.001 HIS B1107 PHE 0.005 0.001 PHE B1135 TYR 0.005 0.001 TYR A1142 ARG 0.001 0.000 ARG A1198 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 152) hydrogen bonds : angle 5.14557 ( 414) SS BOND : bond 0.00212 ( 29) SS BOND : angle 0.84743 ( 58) covalent geometry : bond 0.00205 ( 5166) covalent geometry : angle 0.45126 ( 7036) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1106 CYS cc_start: 0.7422 (m) cc_final: 0.6681 (t) REVERT: A 1122 ASP cc_start: 0.8309 (t0) cc_final: 0.7959 (t0) REVERT: B 1106 CYS cc_start: 0.7405 (m) cc_final: 0.6678 (t) REVERT: B 1122 ASP cc_start: 0.8301 (t0) cc_final: 0.7950 (t0) outliers start: 6 outliers final: 4 residues processed: 24 average time/residue: 0.3335 time to fit residues: 9.8850 Evaluate side-chains 21 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1011 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 51.3153 > 50: distance: 60 - 138: 8.234 distance: 74 - 122: 6.463 distance: 77 - 119: 6.084 distance: 104 - 105: 9.969 distance: 105 - 106: 15.321 distance: 105 - 108: 14.382 distance: 106 - 107: 23.528 distance: 106 - 112: 13.781 distance: 108 - 109: 20.275 distance: 109 - 110: 7.222 distance: 109 - 111: 14.465 distance: 112 - 113: 6.978 distance: 113 - 114: 10.044 distance: 113 - 116: 17.578 distance: 114 - 115: 10.419 distance: 114 - 119: 4.730 distance: 115 - 213: 16.564 distance: 116 - 117: 12.938 distance: 116 - 118: 19.300 distance: 119 - 120: 4.926 distance: 120 - 121: 5.842 distance: 120 - 123: 4.753 distance: 121 - 122: 3.164 distance: 121 - 127: 3.605 distance: 123 - 124: 5.230 distance: 124 - 125: 7.714 distance: 124 - 126: 4.597 distance: 127 - 128: 3.006 distance: 127 - 199: 7.609 distance: 128 - 129: 3.151 distance: 128 - 131: 4.333 distance: 129 - 130: 5.465 distance: 129 - 135: 6.860 distance: 130 - 196: 7.553 distance: 132 - 133: 7.772 distance: 132 - 134: 6.485 distance: 135 - 136: 3.383 distance: 136 - 137: 6.294 distance: 136 - 139: 4.776 distance: 137 - 138: 11.126 distance: 139 - 140: 5.080 distance: 140 - 142: 6.760 distance: 141 - 143: 5.812 distance: 142 - 144: 3.343 distance: 142 - 145: 5.247 distance: 143 - 144: 3.263 distance: 144 - 146: 4.406 distance: 145 - 147: 5.799 distance: 147 - 148: 5.099 distance: 150 - 151: 7.257 distance: 150 - 153: 9.362 distance: 151 - 152: 8.353 distance: 151 - 157: 3.706 distance: 153 - 154: 8.857 distance: 154 - 155: 10.708 distance: 154 - 156: 13.215 distance: 157 - 158: 9.762 distance: 158 - 159: 4.684 distance: 158 - 161: 3.498 distance: 159 - 160: 4.347 distance: 159 - 166: 3.888 distance: 161 - 162: 6.200 distance: 162 - 163: 11.673 distance: 163 - 164: 15.226 distance: 164 - 165: 17.460 distance: 166 - 167: 9.753 distance: 167 - 170: 9.807 distance: 168 - 169: 3.334 distance: 170 - 171: 12.526 distance: 171 - 172: 13.995 distance: 172 - 173: 13.180 distance: 173 - 174: 6.366 distance: 175 - 176: 8.445 distance: 176 - 179: 12.754 distance: 177 - 178: 4.228 distance: 177 - 182: 7.762 distance: 179 - 181: 12.713 distance: 182 - 183: 3.486 distance: 183 - 186: 5.675 distance: 184 - 185: 3.406 distance: 184 - 188: 3.067 distance: 186 - 187: 7.254