Starting phenix.real_space_refine on Sat Aug 3 07:31:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlb_34871/08_2024/8hlb_34871.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlb_34871/08_2024/8hlb_34871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlb_34871/08_2024/8hlb_34871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlb_34871/08_2024/8hlb_34871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlb_34871/08_2024/8hlb_34871.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlb_34871/08_2024/8hlb_34871.cif" } resolution = 3.63 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 4672 2.51 5 N 1257 2.21 5 O 1494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7461 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 868 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "B" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1622 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 203} Chain: "C" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1662 Classifications: {'peptide': 216} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 203} Chain: "D" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1675 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1634 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 201} Time building chain proxies: 4.75, per 1000 atoms: 0.64 Number of scatterers: 7461 At special positions: 0 Unit cell: (65.25, 97.875, 130.5, 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 38 16.00 O 1494 8.00 N 1257 7.00 C 4672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 31 " distance=2.03 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 45 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 115 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " 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: 2.72 Conformation dependent library (CDL) restraints added in 1.3 seconds 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 25 sheets defined 5.4% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 189 through 193 removed outlier: 3.684A pdb=" N SER B 192 " --> pdb=" O PRO B 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.875A pdb=" N SER D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.587A pdb=" N GLY D 139 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 191 through 196 removed outlier: 4.298A pdb=" N GLY D 196 " --> pdb=" O SER D 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.668A pdb=" N HIS E 189 " --> pdb=" O TYR E 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 43 removed outlier: 7.219A pdb=" N VAL A 52 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 58 removed outlier: 5.080A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N MET B 50 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL B 34 " --> pdb=" O MET B 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 128 removed outlier: 6.101A pdb=" N TYR B 180 " --> pdb=" O ASP B 148 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 181 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 158 removed outlier: 4.320A pdb=" N TYR B 198 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7 removed outlier: 4.056A pdb=" N CYS C 23 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE C 75 " --> pdb=" O CYS C 23 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 76 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.790A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AB3, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AB4, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.584A pdb=" N SER C 181 " --> pdb=" O CYS C 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 158 removed outlier: 3.678A pdb=" N GLN C 151 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AB7, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.580A pdb=" N LEU D 115 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.580A pdb=" N LEU D 115 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 126 through 129 removed outlier: 3.822A pdb=" N PHE D 128 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER D 186 " --> pdb=" O CYS D 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 158 through 160 Processing sheet with id=AC2, first strand: chain 'D' and resid 175 through 176 removed outlier: 3.539A pdb=" N SER D 183 " --> pdb=" O VAL D 175 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 12 through 13 Processing sheet with id=AC4, first strand: chain 'E' and resid 22 through 24 removed outlier: 3.712A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.311A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR E 102 " --> pdb=" O TYR E 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 117 Processing sheet with id=AC7, first strand: chain 'E' and resid 144 through 150 177 hydrogen bonds defined for protein. 411 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: 1.91 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2354 1.34 - 1.46: 1570 1.46 - 1.58: 3668 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 7636 Sorted by residual: bond pdb=" N GLN A 82 " pdb=" CA GLN A 82 " ideal model delta sigma weight residual 1.461 1.489 -0.028 1.19e-02 7.06e+03 5.65e+00 bond pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.52e-02 4.33e+03 4.36e+00 bond pdb=" C TYR E 36 " pdb=" N GLN E 37 " ideal model delta sigma weight residual 1.330 1.303 0.027 1.39e-02 5.18e+03 3.74e+00 bond pdb=" N TYR E 36 " pdb=" CA TYR E 36 " ideal model delta sigma weight residual 1.455 1.476 -0.021 1.23e-02 6.61e+03 2.89e+00 bond pdb=" C GLU D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.12e-02 7.97e+03 2.44e+00 ... (remaining 7631 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.10: 261 107.10 - 113.88: 4303 113.88 - 120.66: 2757 120.66 - 127.45: 2986 127.45 - 134.23: 85 Bond angle restraints: 10392 Sorted by residual: angle pdb=" C SER A 79 " pdb=" CA SER A 79 " pdb=" CB SER A 79 " ideal model delta sigma weight residual 116.63 110.25 6.38 1.16e+00 7.43e-01 3.03e+01 angle pdb=" CA SER A 79 " pdb=" C SER A 79 " pdb=" N SER A 80 " ideal model delta sigma weight residual 119.63 116.78 2.85 8.10e-01 1.52e+00 1.24e+01 angle pdb=" CA GLN E 89 " pdb=" C GLN E 89 " pdb=" O GLN E 89 " ideal model delta sigma weight residual 121.06 117.19 3.87 1.16e+00 7.43e-01 1.11e+01 angle pdb=" C GLN E 89 " pdb=" CA GLN E 89 " pdb=" CB GLN E 89 " ideal model delta sigma weight residual 109.56 102.50 7.06 2.22e+00 2.03e-01 1.01e+01 angle pdb=" O TYR D 103 " pdb=" C TYR D 103 " pdb=" N VAL D 104 " ideal model delta sigma weight residual 122.25 125.97 -3.72 1.18e+00 7.18e-01 9.93e+00 ... (remaining 10387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 4110 16.01 - 32.02: 353 32.02 - 48.04: 113 48.04 - 64.05: 17 64.05 - 80.06: 10 Dihedral angle restraints: 4603 sinusoidal: 1769 harmonic: 2834 Sorted by residual: dihedral pdb=" CB CYS A 98 " pdb=" SG CYS A 98 " pdb=" SG CYS A 115 " pdb=" CB CYS A 115 " ideal model delta sinusoidal sigma weight residual 93.00 162.36 -69.36 1 1.00e+01 1.00e-02 6.22e+01 dihedral pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " pdb=" SG CYS A 112 " pdb=" CB CYS A 112 " ideal model delta sinusoidal sigma weight residual 93.00 161.10 -68.10 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CB CYS A 18 " pdb=" SG CYS A 18 " pdb=" SG CYS A 31 " pdb=" CB CYS A 31 " ideal model delta sinusoidal sigma weight residual 93.00 160.13 -67.13 1 1.00e+01 1.00e-02 5.87e+01 ... (remaining 4600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 894 0.043 - 0.087: 187 0.087 - 0.130: 83 0.130 - 0.173: 6 0.173 - 0.216: 2 Chirality restraints: 1172 Sorted by residual: chirality pdb=" CA GLN E 89 " pdb=" N GLN E 89 " pdb=" C GLN E 89 " pdb=" CB GLN E 89 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA ILE D 48 " pdb=" N ILE D 48 " pdb=" C ILE D 48 " pdb=" CB ILE D 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 1169 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 43 " 0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO E 44 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO E 44 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO E 44 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 80 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO C 81 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 81 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 81 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 38 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C GLN E 38 " -0.032 2.00e-02 2.50e+03 pdb=" O GLN E 38 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS E 39 " 0.010 2.00e-02 2.50e+03 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 666 2.74 - 3.28: 7361 3.28 - 3.82: 11738 3.82 - 4.36: 13697 4.36 - 4.90: 23984 Nonbonded interactions: 57446 Sorted by model distance: nonbonded pdb=" O ILE C 110 " pdb=" OH TYR C 144 " model vdw 2.204 3.040 nonbonded pdb=" O ASP A 81 " pdb=" OH TYR D 103 " model vdw 2.214 3.040 nonbonded pdb=" O SER E 30 " pdb=" OH TYR E 71 " model vdw 2.238 3.040 nonbonded pdb=" O VAL C 29 " pdb=" ND2 ASN C 96 " model vdw 2.256 3.120 nonbonded pdb=" OG SER E 121 " pdb=" OE1 GLU E 123 " model vdw 2.277 3.040 ... (remaining 57441 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=1.00 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: 0.840 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.530 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7636 Z= 0.199 Angle : 0.654 8.026 10392 Z= 0.353 Chirality : 0.044 0.216 1172 Planarity : 0.005 0.100 1327 Dihedral : 13.637 80.061 2739 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.38 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 9.43 % 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: -2.13 (0.27), residues: 967 helix: -0.35 (1.20), residues: 22 sheet: -0.98 (0.28), residues: 362 loop : -1.78 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 52 HIS 0.003 0.001 HIS E 90 PHE 0.021 0.002 PHE E 139 TYR 0.021 0.002 TYR E 140 ARG 0.004 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.917 Fit side-chains REVERT: B 86 GLN cc_start: 0.7289 (mm-40) cc_final: 0.7055 (mp10) REVERT: C 2 ILE cc_start: 0.8155 (mm) cc_final: 0.7927 (mm) REVERT: C 52 ILE cc_start: 0.9261 (mm) cc_final: 0.9059 (mm) REVERT: C 135 SER cc_start: 0.7864 (p) cc_final: 0.7603 (p) REVERT: C 149 LYS cc_start: 0.8001 (tttm) cc_final: 0.7631 (tttm) REVERT: C 174 ASP cc_start: 0.8622 (p0) cc_final: 0.8245 (p0) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1886 time to fit residues: 35.3105 Evaluate side-chains 119 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 82 GLN B 3 GLN B 175 GLN C 93 GLN C 162 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 HIS E 147 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 7636 Z= 0.520 Angle : 0.795 8.208 10392 Z= 0.424 Chirality : 0.051 0.208 1172 Planarity : 0.006 0.066 1327 Dihedral : 5.469 26.365 1048 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.00 % Favored : 87.59 % Rotamer: Outliers : 1.41 % Allowed : 12.10 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % 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: -2.54 (0.27), residues: 967 helix: -0.29 (1.16), residues: 22 sheet: -1.16 (0.29), residues: 338 loop : -2.14 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 107 HIS 0.014 0.003 HIS E 90 PHE 0.020 0.003 PHE B 79 TYR 0.052 0.003 TYR B 102 ARG 0.004 0.001 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: B 86 GLN cc_start: 0.7354 (mm-40) cc_final: 0.7031 (mp10) REVERT: B 101 ARG cc_start: 0.6221 (mmm160) cc_final: 0.5800 (mmm160) REVERT: C 57 ASN cc_start: 0.8116 (m-40) cc_final: 0.7901 (m-40) REVERT: C 135 SER cc_start: 0.8320 (p) cc_final: 0.8101 (p) REVERT: C 174 ASP cc_start: 0.8540 (p0) cc_final: 0.8034 (p0) REVERT: C 176 THR cc_start: 0.7630 (m) cc_final: 0.7185 (m) REVERT: E 98 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7659 (m-10) REVERT: E 147 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.7032 (tt0) REVERT: E 195 GLU cc_start: 0.7766 (pp20) cc_final: 0.7325 (pp20) outliers start: 12 outliers final: 6 residues processed: 139 average time/residue: 0.1805 time to fit residues: 34.3774 Evaluate side-chains 129 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 147 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN C 162 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7636 Z= 0.249 Angle : 0.653 7.036 10392 Z= 0.341 Chirality : 0.045 0.189 1172 Planarity : 0.005 0.050 1327 Dihedral : 5.114 23.734 1048 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.07 % Favored : 91.52 % Rotamer: Outliers : 2.70 % Allowed : 13.63 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % 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: -2.40 (0.27), residues: 967 helix: -0.30 (1.13), residues: 22 sheet: -1.08 (0.29), residues: 334 loop : -2.03 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 67 HIS 0.006 0.001 HIS C 38 PHE 0.018 0.002 PHE B 79 TYR 0.031 0.002 TYR B 102 ARG 0.002 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6893 (ttm) cc_final: 0.6215 (ttm) REVERT: B 101 ARG cc_start: 0.6163 (mmm160) cc_final: 0.5015 (mmm160) REVERT: C 52 ILE cc_start: 0.9388 (mm) cc_final: 0.9143 (mm) REVERT: C 135 SER cc_start: 0.8156 (p) cc_final: 0.7921 (p) REVERT: C 149 LYS cc_start: 0.7842 (tttm) cc_final: 0.7580 (tttm) REVERT: C 174 ASP cc_start: 0.8603 (p0) cc_final: 0.8123 (p0) REVERT: E 92 TYR cc_start: 0.7166 (m-80) cc_final: 0.6711 (m-80) REVERT: E 195 GLU cc_start: 0.7647 (pp20) cc_final: 0.7297 (pp20) outliers start: 23 outliers final: 14 residues processed: 140 average time/residue: 0.1809 time to fit residues: 35.0330 Evaluate side-chains 132 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 152 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 0.0470 chunk 77 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7636 Z= 0.202 Angle : 0.635 9.508 10392 Z= 0.327 Chirality : 0.044 0.145 1172 Planarity : 0.005 0.045 1327 Dihedral : 4.906 22.315 1048 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.17 % Favored : 91.42 % Rotamer: Outliers : 2.35 % Allowed : 15.04 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % 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: -2.24 (0.27), residues: 967 helix: -0.16 (1.13), residues: 22 sheet: -0.96 (0.29), residues: 326 loop : -1.92 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 67 HIS 0.005 0.001 HIS E 91 PHE 0.017 0.002 PHE B 79 TYR 0.025 0.002 TYR B 102 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.6858 (ttm) cc_final: 0.6122 (ttm) REVERT: A 39 GLN cc_start: 0.6872 (tt0) cc_final: 0.6493 (tt0) REVERT: B 70 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7563 (p) REVERT: B 79 PHE cc_start: 0.5777 (p90) cc_final: 0.5216 (p90) REVERT: B 101 ARG cc_start: 0.6046 (mmm160) cc_final: 0.4950 (mmm160) REVERT: C 52 ILE cc_start: 0.9358 (mm) cc_final: 0.9133 (mm) REVERT: C 57 ASN cc_start: 0.7887 (m-40) cc_final: 0.7662 (m110) REVERT: C 174 ASP cc_start: 0.8616 (p0) cc_final: 0.8146 (p0) REVERT: E 38 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: E 107 GLN cc_start: 0.7752 (pp30) cc_final: 0.7539 (pp30) REVERT: E 118 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7445 (p90) REVERT: E 195 GLU cc_start: 0.7709 (pp20) cc_final: 0.7281 (pp20) outliers start: 20 outliers final: 14 residues processed: 138 average time/residue: 0.1695 time to fit residues: 32.4217 Evaluate side-chains 136 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-dev-5409/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-dev-5409/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: 64.3892 > 50: distance: 83 - 168: 25.189 distance: 99 - 154: 7.263 distance: 102 - 151: 12.730 distance: 120 - 125: 12.643 distance: 125 - 126: 17.203 distance: 126 - 127: 19.716 distance: 127 - 128: 22.531 distance: 127 - 129: 8.860 distance: 129 - 130: 11.850 distance: 130 - 131: 12.626 distance: 130 - 133: 15.060 distance: 131 - 132: 20.842 distance: 131 - 138: 52.495 distance: 133 - 134: 10.875 distance: 134 - 135: 24.556 distance: 135 - 136: 12.475 distance: 135 - 137: 19.583 distance: 138 - 139: 5.883 distance: 139 - 140: 13.601 distance: 139 - 142: 29.784 distance: 140 - 141: 11.716 distance: 140 - 144: 9.423 distance: 142 - 143: 3.431 distance: 144 - 145: 16.057 distance: 144 - 150: 28.273 distance: 145 - 146: 6.565 distance: 145 - 148: 29.735 distance: 146 - 147: 10.475 distance: 146 - 151: 8.201 distance: 148 - 149: 17.958 distance: 149 - 150: 29.397 distance: 151 - 152: 18.010 distance: 152 - 153: 10.083 distance: 152 - 155: 14.600 distance: 153 - 154: 14.849 distance: 153 - 160: 24.659 distance: 155 - 156: 16.310 distance: 156 - 157: 21.709 distance: 157 - 158: 42.546 distance: 158 - 159: 12.381 distance: 160 - 161: 10.425 distance: 161 - 162: 13.945 distance: 161 - 164: 10.652 distance: 162 - 163: 15.030 distance: 162 - 168: 13.588 distance: 164 - 165: 8.777 distance: 165 - 166: 10.432 distance: 165 - 167: 16.441 distance: 168 - 169: 9.158 distance: 169 - 170: 7.579 distance: 169 - 172: 33.563 distance: 170 - 171: 17.714 distance: 170 - 176: 19.336 distance: 172 - 173: 5.642 distance: 173 - 174: 5.670 distance: 173 - 175: 13.539 distance: 176 - 177: 6.267 distance: 177 - 178: 9.067 distance: 177 - 180: 11.711 distance: 178 - 179: 11.558 distance: 178 - 184: 20.395 distance: 180 - 181: 4.071 distance: 180 - 182: 5.597 distance: 181 - 183: 16.658 distance: 184 - 185: 8.585 distance: 184 - 226: 15.498 distance: 185 - 186: 9.990 distance: 185 - 188: 5.968 distance: 186 - 187: 9.501 distance: 186 - 196: 9.220 distance: 187 - 223: 27.483 distance: 188 - 189: 4.607 distance: 189 - 190: 7.771 distance: 189 - 191: 8.093 distance: 190 - 192: 17.477 distance: 191 - 193: 5.585 distance: 192 - 194: 3.483 distance: 193 - 194: 9.487 distance: 194 - 195: 19.260 distance: 196 - 197: 33.987 distance: 197 - 198: 22.067 distance: 197 - 200: 15.806 distance: 198 - 199: 4.020 distance: 198 - 210: 27.559 distance: 200 - 201: 13.103 distance: 201 - 202: 15.670 distance: 201 - 203: 21.846 distance: 202 - 204: 7.917 distance: 203 - 205: 10.816 distance: 203 - 206: 12.604 distance: 204 - 205: 21.371 distance: 205 - 207: 15.495 distance: 206 - 208: 8.186 distance: 207 - 209: 10.522 distance: 208 - 209: 4.429