Starting phenix.real_space_refine on Thu Dec 7 17:06:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/12_2023/7ymj_33930_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/12_2023/7ymj_33930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/12_2023/7ymj_33930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/12_2023/7ymj_33930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/12_2023/7ymj_33930_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/12_2023/7ymj_33930_updated.pdb" } resolution = 3.35 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= 0.170 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2022 2.51 5 N 511 2.21 5 O 532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 215": "NH1" <-> "NH2" Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3085 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2215 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 265} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 842 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'JGX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.11, per 1000 atoms: 0.68 Number of scatterers: 3085 At special positions: 0 Unit cell: (63.64, 63.64, 127.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 532 8.00 N 511 7.00 C 2022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 97 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.19 Conformation dependent library (CDL) restraints added in 564.4 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 3 sheets defined 53.5% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 26 through 53 removed outlier: 3.924A pdb=" N LEU A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 78 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 98 through 129 removed outlier: 3.799A pdb=" N ALA A 103 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 137 No H-bonds generated for 'chain 'A' and resid 134 through 137' Processing helix chain 'A' and resid 140 through 159 removed outlier: 3.710A pdb=" N ILE A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 182 through 192 Processing helix chain 'A' and resid 194 through 213 removed outlier: 4.010A pdb=" N ALA A 198 " --> pdb=" O TYR A 194 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 297 removed outlier: 4.544A pdb=" N ARG A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Proline residue: A 287 - end of helix Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 314 through 328 removed outlier: 3.986A pdb=" N SER A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Proline residue: A 323 - end of helix removed outlier: 4.882A pdb=" N TYR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 332 through 342 Processing sheet with id= A, first strand: chain 'D' and resid 5 through 9 removed outlier: 3.856A pdb=" N SER D 72 " --> pdb=" O TYR D 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 93 through 95 removed outlier: 3.762A pdb=" N ALA D 93 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 119 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 110 through 113 removed outlier: 3.536A pdb=" N LEU D 110 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR D 101 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 99 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN D 98 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY D 37 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP D 35 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ARG D 102 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU D 33 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET D 36 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 53 " --> pdb=" O MET D 36 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) 157 hydrogen bonds defined for protein. 456 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: 0.70 Time building geometry restraints manager: 1.22 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: 946 1.35 - 1.47: 830 1.47 - 1.59: 1356 1.59 - 1.71: 1 1.71 - 1.83: 26 Bond restraints: 3159 Sorted by residual: bond pdb=" C19 JGX A 401 " pdb=" O26 JGX A 401 " ideal model delta sigma weight residual 1.338 1.399 -0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" C9 JGX A 401 " pdb=" O10 JGX A 401 " ideal model delta sigma weight residual 1.347 1.406 -0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" N25 JGX A 401 " pdb=" S22 JGX A 401 " ideal model delta sigma weight residual 1.653 1.706 -0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C4 JGX A 401 " pdb=" O3 JGX A 401 " ideal model delta sigma weight residual 1.346 1.398 -0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" C20 JGX A 401 " pdb=" S22 JGX A 401 " ideal model delta sigma weight residual 1.771 1.821 -0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 3154 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.93: 85 106.93 - 113.74: 1722 113.74 - 120.54: 1355 120.54 - 127.35: 1106 127.35 - 134.15: 37 Bond angle restraints: 4305 Sorted by residual: angle pdb=" O23 JGX A 401 " pdb=" S22 JGX A 401 " pdb=" O24 JGX A 401 " ideal model delta sigma weight residual 118.38 100.13 18.25 3.00e+00 1.11e-01 3.70e+01 angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 109.81 117.45 -7.64 2.21e+00 2.05e-01 1.20e+01 angle pdb=" N LEU A 286 " pdb=" CA LEU A 286 " pdb=" C LEU A 286 " ideal model delta sigma weight residual 109.81 117.44 -7.63 2.21e+00 2.05e-01 1.19e+01 angle pdb=" N ASN A 322 " pdb=" CA ASN A 322 " pdb=" C ASN A 322 " ideal model delta sigma weight residual 113.16 117.88 -4.72 1.42e+00 4.96e-01 1.11e+01 angle pdb=" N TYR A 326 " pdb=" CA TYR A 326 " pdb=" C TYR A 326 " ideal model delta sigma weight residual 109.81 116.37 -6.56 2.21e+00 2.05e-01 8.82e+00 ... (remaining 4300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 1598 15.85 - 31.70: 177 31.70 - 47.54: 58 47.54 - 63.39: 7 63.39 - 79.24: 1 Dihedral angle restraints: 1841 sinusoidal: 702 harmonic: 1139 Sorted by residual: dihedral pdb=" CA ASP D 74 " pdb=" CB ASP D 74 " pdb=" CG ASP D 74 " pdb=" OD1 ASP D 74 " ideal model delta sinusoidal sigma weight residual -30.00 -84.82 54.82 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA GLU A 180 " pdb=" CB GLU A 180 " pdb=" CG GLU A 180 " pdb=" CD GLU A 180 " ideal model delta sinusoidal sigma weight residual 60.00 107.24 -47.24 3 1.50e+01 4.44e-03 8.46e+00 dihedral pdb=" N LEU A 283 " pdb=" CA LEU A 283 " pdb=" CB LEU A 283 " pdb=" CG LEU A 283 " ideal model delta sinusoidal sigma weight residual -60.00 -106.50 46.50 3 1.50e+01 4.44e-03 8.35e+00 ... (remaining 1838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 307 0.039 - 0.079: 137 0.079 - 0.118: 33 0.118 - 0.158: 20 0.158 - 0.197: 4 Chirality restraints: 501 Sorted by residual: chirality pdb=" CB VAL A 214 " pdb=" CA VAL A 214 " pdb=" CG1 VAL A 214 " pdb=" CG2 VAL A 214 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CB ILE A 159 " pdb=" CA ILE A 159 " pdb=" CG1 ILE A 159 " pdb=" CG2 ILE A 159 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CA GLU A 173 " pdb=" N GLU A 173 " pdb=" C GLU A 173 " pdb=" CB GLU A 173 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 498 not shown) Planarity restraints: 527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 80 " -0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO A 81 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 167 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 168 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 326 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 327 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.030 5.00e-02 4.00e+02 ... (remaining 524 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1043 2.86 - 3.37: 2497 3.37 - 3.88: 4472 3.88 - 4.39: 4722 4.39 - 4.90: 8921 Nonbonded interactions: 21655 Sorted by model distance: nonbonded pdb=" OG SER D 9 " pdb=" OG SER D 23 " model vdw 2.349 2.440 nonbonded pdb=" O SER A 218 " pdb=" OG SER A 218 " model vdw 2.371 2.440 nonbonded pdb=" O GLY A 40 " pdb=" ND2 ASN A 44 " model vdw 2.391 2.520 nonbonded pdb=" N ASP D 111 " pdb=" OD1 ASP D 111 " model vdw 2.495 2.520 nonbonded pdb=" OD2 ASP A 72 " pdb=" NH1 ARG A 113 " model vdw 2.501 2.520 ... (remaining 21650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=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: 0.740 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: 3.600 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.920 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3159 Z= 0.325 Angle : 0.953 18.250 4305 Z= 0.486 Chirality : 0.052 0.197 501 Planarity : 0.007 0.068 527 Dihedral : 14.746 79.241 1107 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % 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: -3.45 (0.34), residues: 390 helix: -1.37 (0.30), residues: 195 sheet: -0.56 (0.77), residues: 50 loop : -4.25 (0.34), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.001 0.001 HIS A 56 PHE 0.023 0.002 PHE A 312 TYR 0.015 0.002 TYR A 204 ARG 0.003 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.351 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1395 time to fit residues: 7.1709 Evaluate side-chains 35 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3159 Z= 0.186 Angle : 0.576 7.670 4305 Z= 0.293 Chirality : 0.041 0.124 501 Planarity : 0.005 0.046 527 Dihedral : 4.960 26.745 456 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.48 % Allowed : 10.25 % Favored : 87.27 % 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: -1.43 (0.42), residues: 390 helix: 0.72 (0.37), residues: 199 sheet: -0.23 (0.81), residues: 50 loop : -3.85 (0.38), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 106 HIS 0.001 0.000 HIS A 56 PHE 0.014 0.001 PHE A 312 TYR 0.014 0.001 TYR A 204 ARG 0.001 0.000 ARG D 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.333 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 0.1011 time to fit residues: 5.7175 Evaluate side-chains 39 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0363 time to fit residues: 0.7810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.0050 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3159 Z= 0.163 Angle : 0.551 8.295 4305 Z= 0.275 Chirality : 0.040 0.121 501 Planarity : 0.004 0.036 527 Dihedral : 3.883 20.960 456 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.93 % Allowed : 14.91 % Favored : 84.16 % 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: -0.53 (0.44), residues: 390 helix: 1.53 (0.38), residues: 199 sheet: 0.28 (0.84), residues: 50 loop : -3.59 (0.41), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.001 0.000 HIS A 56 PHE 0.015 0.001 PHE A 312 TYR 0.013 0.001 TYR A 204 ARG 0.001 0.000 ARG D 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.337 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.1058 time to fit residues: 5.4031 Evaluate side-chains 34 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.296 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0314 time to fit residues: 0.5393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3159 Z= 0.219 Angle : 0.573 6.523 4305 Z= 0.291 Chirality : 0.042 0.121 501 Planarity : 0.004 0.032 527 Dihedral : 3.875 22.394 456 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.80 % Allowed : 14.91 % Favored : 82.30 % 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: -0.29 (0.45), residues: 390 helix: 1.69 (0.38), residues: 199 sheet: 0.38 (0.85), residues: 50 loop : -3.40 (0.43), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 106 HIS 0.001 0.000 HIS A 56 PHE 0.015 0.001 PHE A 312 TYR 0.016 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.351 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 35 average time/residue: 0.1018 time to fit residues: 4.9559 Evaluate side-chains 37 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0365 time to fit residues: 0.8456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.0270 chunk 33 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3159 Z= 0.168 Angle : 0.531 6.307 4305 Z= 0.269 Chirality : 0.040 0.119 501 Planarity : 0.003 0.030 527 Dihedral : 3.683 21.768 456 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.93 % Allowed : 16.77 % Favored : 82.30 % 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: 0.01 (0.45), residues: 390 helix: 1.97 (0.38), residues: 198 sheet: 0.40 (0.84), residues: 52 loop : -3.29 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.001 0.000 HIS A 56 PHE 0.016 0.001 PHE A 312 TYR 0.013 0.001 TYR A 204 ARG 0.001 0.000 ARG D 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.327 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 33 average time/residue: 0.1168 time to fit residues: 5.3894 Evaluate side-chains 31 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0311 time to fit residues: 0.5139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3159 Z= 0.194 Angle : 0.547 6.419 4305 Z= 0.279 Chirality : 0.041 0.119 501 Planarity : 0.003 0.028 527 Dihedral : 3.682 22.230 456 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.48 % Allowed : 16.77 % Favored : 80.75 % 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: 0.12 (0.45), residues: 390 helix: 1.97 (0.37), residues: 199 sheet: 0.56 (0.83), residues: 52 loop : -3.15 (0.45), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 106 HIS 0.001 0.000 HIS A 56 PHE 0.016 0.001 PHE A 312 TYR 0.015 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.343 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 34 average time/residue: 0.1045 time to fit residues: 4.9608 Evaluate side-chains 36 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.292 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0333 time to fit residues: 0.7025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.4636 > 50: distance: 37 - 144: 9.435 distance: 76 - 158: 20.226 distance: 98 - 130: 5.764 distance: 101 - 127: 5.954 distance: 123 - 127: 4.610 distance: 127 - 128: 3.519 distance: 128 - 129: 4.391 distance: 128 - 131: 15.465 distance: 129 - 130: 7.904 distance: 129 - 139: 8.447 distance: 132 - 133: 5.919 distance: 132 - 134: 9.594 distance: 133 - 135: 7.921 distance: 134 - 136: 11.606 distance: 135 - 137: 4.954 distance: 136 - 137: 3.837 distance: 137 - 138: 16.783 distance: 139 - 140: 5.316 distance: 140 - 141: 6.089 distance: 140 - 143: 12.018 distance: 141 - 142: 10.509 distance: 141 - 145: 7.815 distance: 143 - 144: 10.853 distance: 145 - 146: 12.051 distance: 146 - 147: 13.694 distance: 146 - 149: 13.317 distance: 147 - 148: 5.160 distance: 147 - 153: 6.200 distance: 149 - 150: 8.880 distance: 150 - 151: 12.570 distance: 150 - 152: 15.972 distance: 153 - 154: 6.111 distance: 154 - 155: 6.594 distance: 154 - 157: 17.112 distance: 155 - 156: 19.230 distance: 155 - 158: 18.741 distance: 156 - 255: 11.494 distance: 158 - 159: 24.984 distance: 159 - 160: 44.778 distance: 159 - 162: 27.878 distance: 160 - 161: 51.895 distance: 160 - 167: 20.136 distance: 162 - 163: 21.842 distance: 163 - 164: 17.590 distance: 164 - 165: 9.492 distance: 164 - 166: 11.521 distance: 167 - 168: 21.308 distance: 168 - 169: 26.884 distance: 168 - 171: 21.570 distance: 169 - 170: 34.222 distance: 169 - 179: 19.910 distance: 171 - 172: 35.775 distance: 172 - 173: 17.452 distance: 172 - 174: 26.513 distance: 173 - 175: 14.594 distance: 174 - 176: 12.445 distance: 175 - 177: 11.563 distance: 176 - 177: 6.649 distance: 177 - 178: 35.375 distance: 179 - 180: 13.559 distance: 180 - 181: 15.435 distance: 180 - 183: 24.044 distance: 181 - 182: 10.788 distance: 181 - 190: 7.221 distance: 183 - 184: 30.427 distance: 184 - 185: 23.605 distance: 185 - 186: 11.401 distance: 186 - 187: 19.986 distance: 187 - 188: 13.575 distance: 187 - 189: 8.161 distance: 190 - 191: 8.139 distance: 191 - 192: 8.830 distance: 191 - 194: 4.963 distance: 192 - 193: 9.761 distance: 192 - 197: 11.043 distance: 194 - 195: 22.212 distance: 194 - 196: 20.527 distance: 197 - 198: 17.783 distance: 198 - 199: 15.491 distance: 199 - 200: 9.509 distance: 199 - 201: 16.986 distance: 201 - 202: 22.369 distance: 202 - 203: 30.343 distance: 202 - 205: 20.844 distance: 203 - 204: 12.704 distance: 203 - 209: 15.691 distance: 205 - 206: 18.518 distance: 205 - 207: 44.957 distance: 206 - 208: 36.521