Starting phenix.real_space_refine on Fri Aug 22 12:39:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbp_61322/08_2025/9jbp_61322_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbp_61322/08_2025/9jbp_61322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jbp_61322/08_2025/9jbp_61322_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbp_61322/08_2025/9jbp_61322_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jbp_61322/08_2025/9jbp_61322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbp_61322/08_2025/9jbp_61322.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1278 2.51 5 N 354 2.21 5 O 390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2022 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 297 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: B, C, D, E, F, H, I, J, K, L Time building chain proxies: 0.31, per 1000 atoms: 0.15 Number of scatterers: 2022 At special positions: 0 Unit cell: (68.04, 103.68, 32.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 390 8.00 N 354 7.00 C 1278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.08 Conformation dependent library (CDL) restraints added in 43.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 504 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.517A pdb=" N GLN A 15 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE B 18 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN B 15 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 17 " --> pdb=" O ILE C 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 35 removed outlier: 6.174A pdb=" N VAL B 31 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SER C 34 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY B 33 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 6 removed outlier: 5.947A pdb=" N UNK G 4 " --> pdb=" O UNK H 5 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N UNK H 4 " --> pdb=" O UNK I 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AA6, first strand: chain 'D' and resid 14 through 18 removed outlier: 5.667A pdb=" N GLN D 15 " --> pdb=" O GLY E 16 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE E 18 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE D 17 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN E 15 " --> pdb=" O GLY F 16 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE F 18 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE E 17 " --> pdb=" O ILE F 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 30 through 35 removed outlier: 6.410A pdb=" N VAL D 31 " --> pdb=" O TRP E 32 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N SER E 34 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY D 33 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL E 31 " --> pdb=" O TRP F 32 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N SER F 34 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY E 33 " --> pdb=" O SER F 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'J' and resid 3 through 6 removed outlier: 6.044A pdb=" N UNK J 4 " --> pdb=" O UNK K 5 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N UNK K 4 " --> pdb=" O UNK L 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 20 hydrogen bonds defined for protein. 60 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: 0.13 Time building geometry restraints manager: 0.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 366 1.29 - 1.35: 306 1.35 - 1.42: 102 1.42 - 1.48: 324 1.48 - 1.54: 942 Bond restraints: 2040 Sorted by residual: bond pdb=" CB VAL E 29 " pdb=" CG1 VAL E 29 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.63e-01 bond pdb=" CB VAL A 29 " pdb=" CG1 VAL A 29 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.57e-01 bond pdb=" CB VAL C 29 " pdb=" CG1 VAL C 29 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.45e-01 bond pdb=" CB VAL B 29 " pdb=" CG1 VAL B 29 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.40e-01 bond pdb=" CB VAL D 29 " pdb=" CG1 VAL D 29 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.39e-01 ... (remaining 2035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 2615 1.44 - 2.89: 121 2.89 - 4.33: 6 4.33 - 5.78: 0 5.78 - 7.22: 6 Bond angle restraints: 2748 Sorted by residual: angle pdb=" CA LEU D 38 " pdb=" CB LEU D 38 " pdb=" CG LEU D 38 " ideal model delta sigma weight residual 116.30 123.52 -7.22 3.50e+00 8.16e-02 4.25e+00 angle pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " pdb=" CG LEU C 38 " ideal model delta sigma weight residual 116.30 123.50 -7.20 3.50e+00 8.16e-02 4.24e+00 angle pdb=" CA LEU E 38 " pdb=" CB LEU E 38 " pdb=" CG LEU E 38 " ideal model delta sigma weight residual 116.30 123.50 -7.20 3.50e+00 8.16e-02 4.23e+00 angle pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " pdb=" CG LEU A 38 " ideal model delta sigma weight residual 116.30 123.49 -7.19 3.50e+00 8.16e-02 4.23e+00 angle pdb=" CA LEU F 38 " pdb=" CB LEU F 38 " pdb=" CG LEU F 38 " ideal model delta sigma weight residual 116.30 123.49 -7.19 3.50e+00 8.16e-02 4.22e+00 ... (remaining 2743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 1052 15.81 - 31.63: 112 31.63 - 47.44: 18 47.44 - 63.26: 18 63.26 - 79.07: 6 Dihedral angle restraints: 1206 sinusoidal: 420 harmonic: 786 Sorted by residual: dihedral pdb=" CA GLN C 15 " pdb=" CB GLN C 15 " pdb=" CG GLN C 15 " pdb=" CD GLN C 15 " ideal model delta sinusoidal sigma weight residual 180.00 142.88 37.12 3 1.50e+01 4.44e-03 6.47e+00 dihedral pdb=" CA GLN F 15 " pdb=" CB GLN F 15 " pdb=" CG GLN F 15 " pdb=" CD GLN F 15 " ideal model delta sinusoidal sigma weight residual 180.00 142.88 37.12 3 1.50e+01 4.44e-03 6.47e+00 dihedral pdb=" CA GLN B 15 " pdb=" CB GLN B 15 " pdb=" CG GLN B 15 " pdb=" CD GLN B 15 " ideal model delta sinusoidal sigma weight residual 180.00 142.89 37.11 3 1.50e+01 4.44e-03 6.47e+00 ... (remaining 1203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 168 0.030 - 0.060: 99 0.060 - 0.091: 9 0.091 - 0.121: 42 0.121 - 0.151: 6 Chirality restraints: 324 Sorted by residual: chirality pdb=" CG LEU A 38 " pdb=" CB LEU A 38 " pdb=" CD1 LEU A 38 " pdb=" CD2 LEU A 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CG LEU F 38 " pdb=" CB LEU F 38 " pdb=" CD1 LEU F 38 " pdb=" CD2 LEU F 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CG LEU E 38 " pdb=" CB LEU E 38 " pdb=" CD1 LEU E 38 " pdb=" CD2 LEU E 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 321 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 12 " -0.010 5.00e-02 4.00e+02 1.50e-02 3.58e-01 pdb=" N PRO B 13 " 0.026 5.00e-02 4.00e+02 pdb=" CA PRO B 13 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO B 13 " -0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 12 " -0.010 5.00e-02 4.00e+02 1.49e-02 3.57e-01 pdb=" N PRO E 13 " 0.026 5.00e-02 4.00e+02 pdb=" CA PRO E 13 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO E 13 " -0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 12 " -0.010 5.00e-02 4.00e+02 1.48e-02 3.49e-01 pdb=" N PRO F 13 " 0.026 5.00e-02 4.00e+02 pdb=" CA PRO F 13 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO F 13 " -0.008 5.00e-02 4.00e+02 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 897 2.92 - 3.41: 1607 3.41 - 3.91: 3159 3.91 - 4.40: 3013 4.40 - 4.90: 6557 Nonbonded interactions: 15233 Sorted by model distance: nonbonded pdb=" ND2 ASN B 26 " pdb=" O ASN C 26 " model vdw 2.424 3.120 nonbonded pdb=" O ALA A 1 " pdb=" N ALA B 1 " model vdw 2.463 3.120 nonbonded pdb=" O ALA D 1 " pdb=" N ALA E 1 " model vdw 2.482 3.120 nonbonded pdb=" ND2 ASN D 26 " pdb=" O ASN E 26 " model vdw 2.514 3.120 nonbonded pdb=" ND2 ASN E 26 " pdb=" O ASN F 26 " model vdw 2.515 3.120 ... (remaining 15228 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.390 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.300 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 4.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 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 0.020 2040 Z= 0.137 Angle : 0.697 7.219 2748 Z= 0.346 Chirality : 0.051 0.151 324 Planarity : 0.003 0.015 354 Dihedral : 16.942 79.069 702 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 25.81 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.57), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.52 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.002 PHE C 20 TRP 0.002 0.000 TRP C 32 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 2040) covalent geometry : angle 0.69663 ( 2748) hydrogen bonds : bond 0.14889 ( 20) hydrogen bonds : angle 8.20527 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0188 time to fit residues: 0.6972 Evaluate side-chains 25 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN B 26 ASN C 26 ASN D 26 ASN E 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6043 r_free = 0.6043 target = 0.398150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.6231 r_free = 0.6231 target = 0.360271 restraints weight = 2573.062| |-----------------------------------------------------------------------------| r_work (start): 0.5503 rms_B_bonded: 1.58 r_work: 0.5353 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.5251 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.5251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 2040 Z= 0.306 Angle : 0.746 5.841 2748 Z= 0.394 Chirality : 0.048 0.116 324 Planarity : 0.005 0.030 354 Dihedral : 4.365 13.617 282 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 8.06 % Allowed : 21.51 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.55), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 20 TRP 0.015 0.003 TRP E 32 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 2040) covalent geometry : angle 0.74589 ( 2748) hydrogen bonds : bond 0.04449 ( 20) hydrogen bonds : angle 5.34496 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.075 Fit side-chains REVERT: F 24 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7602 (tt0) outliers start: 15 outliers final: 14 residues processed: 44 average time/residue: 0.0255 time to fit residues: 1.5868 Evaluate side-chains 48 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN B 26 ASN C 15 GLN C 26 ASN D 26 ASN E 15 GLN E 26 ASN F 15 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6119 r_free = 0.6119 target = 0.449524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.6422 r_free = 0.6422 target = 0.378701 restraints weight = 2777.260| |-----------------------------------------------------------------------------| r_work (start): 0.5648 rms_B_bonded: 1.55 r_work: 0.5516 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.5421 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.5421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2040 Z= 0.110 Angle : 0.488 3.873 2748 Z= 0.256 Chirality : 0.045 0.117 324 Planarity : 0.003 0.021 354 Dihedral : 3.304 10.505 282 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.84 % Allowed : 24.19 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.54), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.78 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE E 20 TRP 0.005 0.001 TRP B 32 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 2040) covalent geometry : angle 0.48837 ( 2748) hydrogen bonds : bond 0.02615 ( 20) hydrogen bonds : angle 4.38562 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.082 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 39 average time/residue: 0.0314 time to fit residues: 1.6518 Evaluate side-chains 39 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN C 26 ASN D 26 ASN E 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6001 r_free = 0.6001 target = 0.398613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.6179 r_free = 0.6179 target = 0.358641 restraints weight = 2578.323| |-----------------------------------------------------------------------------| r_work (start): 0.5491 rms_B_bonded: 1.64 r_work: 0.5330 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.5231 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.5231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2040 Z= 0.270 Angle : 0.675 4.472 2748 Z= 0.362 Chirality : 0.047 0.125 324 Planarity : 0.004 0.028 354 Dihedral : 4.310 12.933 282 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 10.22 % Allowed : 22.04 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.52), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.002 PHE F 20 TRP 0.013 0.003 TRP A 32 Details of bonding type rmsd covalent geometry : bond 0.00606 ( 2040) covalent geometry : angle 0.67542 ( 2748) hydrogen bonds : bond 0.03347 ( 20) hydrogen bonds : angle 4.53058 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.080 Fit side-chains REVERT: F 24 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7610 (tt0) outliers start: 19 outliers final: 16 residues processed: 46 average time/residue: 0.0353 time to fit residues: 2.0960 Evaluate side-chains 47 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.0010 chunk 22 optimal weight: 0.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN C 26 ASN D 26 ASN E 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6074 r_free = 0.6074 target = 0.410411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.6266 r_free = 0.6266 target = 0.372286 restraints weight = 2589.567| |-----------------------------------------------------------------------------| r_work (start): 0.5626 rms_B_bonded: 1.67 r_work: 0.5489 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.5389 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.5389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2040 Z= 0.106 Angle : 0.500 4.428 2748 Z= 0.266 Chirality : 0.045 0.120 324 Planarity : 0.003 0.019 354 Dihedral : 3.367 10.571 282 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.38 % Allowed : 26.88 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.51), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE E 20 TRP 0.004 0.001 TRP F 32 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 2040) covalent geometry : angle 0.50025 ( 2748) hydrogen bonds : bond 0.02046 ( 20) hydrogen bonds : angle 4.07292 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.080 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 33 average time/residue: 0.0248 time to fit residues: 1.1721 Evaluate side-chains 38 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.1146 > 50: distance: 119 - 123: 22.380 distance: 123 - 124: 9.561 distance: 124 - 125: 17.331 distance: 125 - 126: 3.400 distance: 125 - 127: 18.432 distance: 127 - 128: 21.365 distance: 128 - 129: 25.589 distance: 128 - 131: 40.899 distance: 129 - 130: 4.103 distance: 129 - 135: 30.778 distance: 131 - 132: 20.555 distance: 132 - 133: 29.365 distance: 132 - 134: 18.223 distance: 135 - 136: 46.795 distance: 136 - 137: 24.827 distance: 137 - 138: 15.999 distance: 139 - 140: 41.391 distance: 139 - 145: 41.118 distance: 140 - 141: 9.287 distance: 140 - 143: 48.529 distance: 141 - 146: 7.396 distance: 143 - 144: 28.063 distance: 144 - 145: 37.084 distance: 146 - 147: 27.126 distance: 147 - 148: 4.329 distance: 147 - 150: 53.948 distance: 148 - 149: 14.168 distance: 148 - 153: 14.627 distance: 150 - 151: 51.118 distance: 150 - 152: 34.518 distance: 153 - 154: 8.301 distance: 154 - 155: 25.626 distance: 154 - 157: 25.831 distance: 155 - 156: 27.747 distance: 155 - 162: 13.864 distance: 158 - 159: 15.846 distance: 159 - 160: 9.208 distance: 159 - 161: 6.278 distance: 162 - 163: 16.941 distance: 163 - 164: 32.862 distance: 164 - 165: 21.399 distance: 164 - 166: 30.849 distance: 166 - 167: 34.345 distance: 167 - 168: 24.819 distance: 167 - 170: 27.547 distance: 168 - 169: 33.605 distance: 168 - 174: 20.760 distance: 170 - 171: 50.552 distance: 170 - 172: 23.898 distance: 171 - 173: 33.312 distance: 174 - 175: 33.691 distance: 175 - 176: 37.115 distance: 175 - 178: 14.213 distance: 176 - 177: 39.845 distance: 176 - 182: 40.144 distance: 178 - 179: 39.614 distance: 178 - 180: 27.750 distance: 179 - 181: 19.189 distance: 182 - 183: 22.031 distance: 183 - 184: 17.864 distance: 183 - 186: 16.081 distance: 184 - 185: 23.272 distance: 184 - 190: 14.716 distance: 186 - 187: 15.655 distance: 187 - 188: 13.042 distance: 187 - 189: 41.819