Starting phenix.real_space_refine on Fri Aug 22 12:39:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kig_37259/08_2025/8kig_37259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kig_37259/08_2025/8kig_37259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kig_37259/08_2025/8kig_37259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kig_37259/08_2025/8kig_37259.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kig_37259/08_2025/8kig_37259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kig_37259/08_2025/8kig_37259.map" } resolution = 3.1 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= -0.001 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 27 5.16 5 C 1405 2.51 5 N 327 2.21 5 O 344 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: 2104 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2025 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 1, 'ASP:plan': 1, '4J2:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.94, per 1000 atoms: 0.45 Number of scatterers: 2104 At special positions: 0 Unit cell: (74.8, 64.6, 79.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 27 16.00 O 344 8.00 N 327 7.00 C 1405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 268 " - pdb=" SG CYS R 274 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 83.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 4J2 L 4 " Number of C-beta restraints generated: 514 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 83.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'R' and resid 41 through 66 removed outlier: 4.125A pdb=" N PHE R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 103 removed outlier: 3.522A pdb=" N ALA R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 121 removed outlier: 3.752A pdb=" N ASN R 118 " --> pdb=" O GLN R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 148 removed outlier: 3.680A pdb=" N VAL R 129 " --> pdb=" O CYS R 125 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER R 131 " --> pdb=" O SER R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 156 Processing helix chain 'R' and resid 157 through 182 removed outlier: 3.794A pdb=" N ILE R 180 " --> pdb=" O GLY R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 211 removed outlier: 3.505A pdb=" N VAL R 190 " --> pdb=" O LYS R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 241 removed outlier: 4.053A pdb=" N ALA R 241 " --> pdb=" O CYS R 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 237 through 241' Processing helix chain 'R' and resid 242 through 265 removed outlier: 3.526A pdb=" N PHE R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE R 252 " --> pdb=" O LEU R 248 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE R 253 " --> pdb=" O GLY R 249 " (cutoff:3.500A) Proline residue: R 257 - end of helix removed outlier: 3.565A pdb=" N HIS R 261 " --> pdb=" O PRO R 257 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU R 262 " --> pdb=" O PHE R 258 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE R 265 " --> pdb=" O HIS R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 279 removed outlier: 3.845A pdb=" N CYS R 276 " --> pdb=" O PRO R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 Processing helix chain 'R' and resid 285 through 291 Processing helix chain 'R' and resid 294 through 301 Processing helix chain 'R' and resid 303 through 315 removed outlier: 3.627A pdb=" N ARG R 307 " --> pdb=" O SER R 303 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 432 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: 0.29 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 604 1.34 - 1.46: 406 1.46 - 1.58: 1101 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 2151 Sorted by residual: bond pdb=" CA 4J2 L 4 " pdb=" C 4J2 L 4 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.10e-02 2.27e+03 2.98e+00 bond pdb=" CG PRO R 72 " pdb=" CD PRO R 72 " ideal model delta sigma weight residual 1.503 1.556 -0.053 3.40e-02 8.65e+02 2.46e+00 bond pdb=" C TYR R 74 " pdb=" O TYR R 74 " ideal model delta sigma weight residual 1.235 1.215 0.021 1.33e-02 5.65e+03 2.39e+00 bond pdb=" N TYR R 74 " pdb=" CA TYR R 74 " ideal model delta sigma weight residual 1.456 1.475 -0.019 1.32e-02 5.74e+03 2.08e+00 bond pdb=" CB 4J2 L 4 " pdb=" CG 4J2 L 4 " ideal model delta sigma weight residual 1.501 1.472 0.029 2.00e-02 2.50e+03 2.06e+00 ... (remaining 2146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 2795 1.46 - 2.92: 101 2.92 - 4.37: 22 4.37 - 5.83: 5 5.83 - 7.29: 3 Bond angle restraints: 2926 Sorted by residual: angle pdb=" CA TYR R 105 " pdb=" C TYR R 105 " pdb=" N LEU R 106 " ideal model delta sigma weight residual 118.22 121.03 -2.81 1.03e+00 9.43e-01 7.46e+00 angle pdb=" CB MET R 289 " pdb=" CG MET R 289 " pdb=" SD MET R 289 " ideal model delta sigma weight residual 112.70 105.60 7.10 3.00e+00 1.11e-01 5.60e+00 angle pdb=" C THR R 107 " pdb=" N PHE R 108 " pdb=" CA PHE R 108 " ideal model delta sigma weight residual 122.50 118.53 3.97 1.82e+00 3.02e-01 4.76e+00 angle pdb=" N VAL R 263 " pdb=" CA VAL R 263 " pdb=" C VAL R 263 " ideal model delta sigma weight residual 113.16 109.94 3.22 1.49e+00 4.50e-01 4.66e+00 angle pdb=" CA LEU R 106 " pdb=" CB LEU R 106 " pdb=" CG LEU R 106 " ideal model delta sigma weight residual 116.30 123.59 -7.29 3.50e+00 8.16e-02 4.34e+00 ... (remaining 2921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 1047 16.43 - 32.86: 159 32.86 - 49.30: 38 49.30 - 65.73: 8 65.73 - 82.16: 2 Dihedral angle restraints: 1254 sinusoidal: 468 harmonic: 786 Sorted by residual: dihedral pdb=" CA GLU R 109 " pdb=" C GLU R 109 " pdb=" N ASP R 110 " pdb=" CA ASP R 110 " ideal model delta harmonic sigma weight residual -180.00 -154.24 -25.76 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA LEU R 262 " pdb=" C LEU R 262 " pdb=" N VAL R 263 " pdb=" CA VAL R 263 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CB CYS R 268 " pdb=" SG CYS R 268 " pdb=" SG CYS R 274 " pdb=" CB CYS R 274 " ideal model delta sinusoidal sigma weight residual -86.00 -122.89 36.89 1 1.00e+01 1.00e-02 1.92e+01 ... (remaining 1251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 196 0.033 - 0.065: 126 0.065 - 0.098: 28 0.098 - 0.131: 7 0.131 - 0.163: 7 Chirality restraints: 364 Sorted by residual: chirality pdb=" CG LEU R 106 " pdb=" CB LEU R 106 " pdb=" CD1 LEU R 106 " pdb=" CD2 LEU R 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CB THR R 194 " pdb=" CA THR R 194 " pdb=" OG1 THR R 194 " pdb=" CG2 THR R 194 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA PRO R 72 " pdb=" N PRO R 72 " pdb=" C PRO R 72 " pdb=" CB PRO R 72 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 361 not shown) Planarity restraints: 344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 71 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO R 72 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO R 72 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 72 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 302 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C ARG R 302 " 0.020 2.00e-02 2.50e+03 pdb=" O ARG R 302 " -0.007 2.00e-02 2.50e+03 pdb=" N SER R 303 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 197 " -0.009 2.00e-02 2.50e+03 6.30e-03 6.95e-01 pdb=" CG PHE R 197 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE R 197 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 197 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 197 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE R 197 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 197 " -0.001 2.00e-02 2.50e+03 ... (remaining 341 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 62 2.69 - 3.24: 2154 3.24 - 3.80: 3228 3.80 - 4.35: 4073 4.35 - 4.90: 6765 Nonbonded interactions: 16282 Sorted by model distance: nonbonded pdb=" O VAL R 263 " pdb=" OG1 THR R 267 " model vdw 2.138 3.040 nonbonded pdb=" OG SER R 52 " pdb=" OG SER R 88 " model vdw 2.146 3.040 nonbonded pdb=" OE2 GLU R 94 " pdb="CA CA R 401 " model vdw 2.173 2.510 nonbonded pdb=" O SER R 127 " pdb=" OG SER R 127 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP R 121 " pdb="CA CA R 401 " model vdw 2.262 2.510 ... (remaining 16277 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 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: 2.350 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.850 Find NCS groups from input model: 0.010 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.007 0.102 2153 Z= 0.354 Angle : 0.719 7.289 2928 Z= 0.370 Chirality : 0.046 0.163 364 Planarity : 0.005 0.066 344 Dihedral : 16.913 82.158 737 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.85 % Allowed : 37.02 % Favored : 62.13 % 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: -0.40 (0.56), residues: 255 helix: 0.14 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -1.55 (1.06), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 302 TYR 0.011 0.002 TYR R 152 PHE 0.014 0.002 PHE R 259 TRP 0.010 0.002 TRP R 169 HIS 0.002 0.001 HIS R 261 Details of bonding type rmsd covalent geometry : bond 0.00653 ( 2151) covalent geometry : angle 0.71890 ( 2926) SS BOND : bond 0.00209 ( 1) SS BOND : angle 1.04727 ( 2) hydrogen bonds : bond 0.20409 ( 146) hydrogen bonds : angle 7.09416 ( 432) Misc. bond : bond 0.10198 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.119 Fit side-chains REVERT: R 307 ARG cc_start: 0.8720 (mtp85) cc_final: 0.8370 (mtm-85) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.1011 time to fit residues: 6.0715 Evaluate side-chains 51 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 145 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.160906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.127427 restraints weight = 2809.658| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.68 r_work: 0.3502 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2153 Z= 0.147 Angle : 0.609 6.385 2928 Z= 0.316 Chirality : 0.041 0.153 364 Planarity : 0.003 0.019 344 Dihedral : 5.125 26.694 286 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.53 % Allowed : 29.79 % Favored : 64.68 % 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: 0.76 (0.56), residues: 255 helix: 0.79 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.65 (1.18), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 302 TYR 0.012 0.001 TYR R 277 PHE 0.018 0.001 PHE R 197 TRP 0.013 0.002 TRP R 169 HIS 0.001 0.000 HIS R 280 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 2151) covalent geometry : angle 0.60882 ( 2926) SS BOND : bond 0.00285 ( 1) SS BOND : angle 0.78704 ( 2) hydrogen bonds : bond 0.04941 ( 146) hydrogen bonds : angle 4.81835 ( 432) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.087 Fit side-chains REVERT: R 184 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5669 (pm20) REVERT: R 197 PHE cc_start: 0.8069 (t80) cc_final: 0.7868 (t80) REVERT: R 307 ARG cc_start: 0.8682 (mtp85) cc_final: 0.8175 (mtm-85) outliers start: 13 outliers final: 3 residues processed: 62 average time/residue: 0.0704 time to fit residues: 5.0543 Evaluate side-chains 57 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.166660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133387 restraints weight = 2763.699| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.64 r_work: 0.3539 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2153 Z= 0.124 Angle : 0.545 6.101 2928 Z= 0.286 Chirality : 0.039 0.127 364 Planarity : 0.003 0.019 344 Dihedral : 4.635 25.556 285 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.68 % Allowed : 30.64 % Favored : 64.68 % 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: 1.46 (0.56), residues: 255 helix: 1.25 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.27 (1.16), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 302 TYR 0.009 0.001 TYR R 152 PHE 0.021 0.001 PHE R 197 TRP 0.010 0.001 TRP R 169 HIS 0.001 0.000 HIS R 280 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 2151) covalent geometry : angle 0.54471 ( 2926) SS BOND : bond 0.00192 ( 1) SS BOND : angle 0.64341 ( 2) hydrogen bonds : bond 0.04215 ( 146) hydrogen bonds : angle 4.25626 ( 432) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.079 Fit side-chains REVERT: R 184 GLU cc_start: 0.5697 (OUTLIER) cc_final: 0.5440 (pm20) REVERT: R 197 PHE cc_start: 0.8036 (t80) cc_final: 0.7796 (t80) REVERT: R 201 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8218 (mp) REVERT: R 307 ARG cc_start: 0.8670 (mtp85) cc_final: 0.8147 (mtm-85) outliers start: 11 outliers final: 4 residues processed: 61 average time/residue: 0.0666 time to fit residues: 4.7187 Evaluate side-chains 60 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.167134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133733 restraints weight = 2717.937| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.64 r_work: 0.3554 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2153 Z= 0.118 Angle : 0.560 7.309 2928 Z= 0.283 Chirality : 0.038 0.138 364 Planarity : 0.003 0.018 344 Dihedral : 4.416 24.622 285 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.96 % Allowed : 28.94 % Favored : 65.11 % 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: 1.85 (0.57), residues: 255 helix: 1.51 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.10 (1.17), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 302 TYR 0.012 0.001 TYR R 277 PHE 0.021 0.001 PHE R 197 TRP 0.008 0.001 TRP R 169 HIS 0.001 0.000 HIS R 280 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 2151) covalent geometry : angle 0.56003 ( 2926) SS BOND : bond 0.00236 ( 1) SS BOND : angle 0.72364 ( 2) hydrogen bonds : bond 0.04003 ( 146) hydrogen bonds : angle 4.01400 ( 432) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.080 Fit side-chains REVERT: R 184 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.5512 (pm20) REVERT: R 201 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8195 (mp) outliers start: 14 outliers final: 7 residues processed: 62 average time/residue: 0.0623 time to fit residues: 4.5183 Evaluate side-chains 60 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 17 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.169129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135657 restraints weight = 2683.939| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.64 r_work: 0.3578 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2153 Z= 0.109 Angle : 0.543 7.488 2928 Z= 0.273 Chirality : 0.038 0.140 364 Planarity : 0.003 0.020 344 Dihedral : 4.254 24.055 285 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.11 % Allowed : 30.64 % Favored : 64.26 % 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: 2.13 (0.57), residues: 255 helix: 1.73 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.20 (1.14), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 302 TYR 0.014 0.001 TYR R 277 PHE 0.014 0.001 PHE R 197 TRP 0.008 0.001 TRP R 169 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 2151) covalent geometry : angle 0.54266 ( 2926) SS BOND : bond 0.00195 ( 1) SS BOND : angle 0.57332 ( 2) hydrogen bonds : bond 0.03745 ( 146) hydrogen bonds : angle 3.88159 ( 432) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.086 Fit side-chains REVERT: R 184 GLU cc_start: 0.5648 (OUTLIER) cc_final: 0.5354 (pm20) REVERT: R 201 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8241 (mp) REVERT: R 289 MET cc_start: 0.8188 (mmm) cc_final: 0.7834 (mmm) REVERT: R 307 ARG cc_start: 0.8631 (mtp85) cc_final: 0.8312 (mtm-85) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 0.0686 time to fit residues: 5.0929 Evaluate side-chains 62 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU 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: 50.1832 > 50: distance: 44 - 66: 4.625 distance: 53 - 74: 5.972 distance: 62 - 90: 6.478 distance: 67 - 68: 3.270 distance: 67 - 70: 5.520 distance: 68 - 69: 7.302 distance: 68 - 74: 6.660 distance: 69 - 98: 11.689 distance: 70 - 71: 7.330 distance: 71 - 72: 6.660 distance: 72 - 73: 7.807 distance: 74 - 75: 7.782 distance: 75 - 76: 11.848 distance: 75 - 78: 7.670 distance: 76 - 77: 5.822 distance: 76 - 82: 7.833 distance: 77 - 109: 11.011 distance: 78 - 79: 8.195 distance: 79 - 80: 6.249 distance: 79 - 81: 4.607 distance: 82 - 83: 5.376 distance: 83 - 84: 6.638 distance: 84 - 85: 3.899 distance: 84 - 90: 3.611 distance: 86 - 87: 6.941 distance: 87 - 88: 9.554 distance: 87 - 89: 12.182 distance: 90 - 91: 8.202 distance: 91 - 92: 8.592 distance: 91 - 94: 7.821 distance: 92 - 98: 7.329 distance: 94 - 95: 9.694 distance: 94 - 96: 10.317 distance: 95 - 97: 8.632 distance: 98 - 99: 4.218 distance: 99 - 100: 4.420 distance: 99 - 102: 5.152 distance: 100 - 101: 4.472 distance: 102 - 103: 3.510 distance: 103 - 104: 6.060 distance: 103 - 105: 8.270 distance: 104 - 106: 6.628 distance: 105 - 107: 7.152 distance: 106 - 108: 8.093 distance: 107 - 108: 3.731 distance: 109 - 110: 11.902 distance: 110 - 111: 3.498 distance: 110 - 113: 12.437 distance: 111 - 112: 3.262 distance: 113 - 114: 3.270 distance: 114 - 115: 3.243 distance: 114 - 116: 4.214 distance: 117 - 118: 6.257 distance: 118 - 119: 8.518 distance: 118 - 121: 6.425 distance: 119 - 120: 9.617 distance: 119 - 123: 4.572 distance: 121 - 122: 8.436 distance: 123 - 124: 10.039 distance: 124 - 125: 9.825 distance: 124 - 127: 5.177 distance: 125 - 126: 25.757 distance: 125 - 131: 26.645 distance: 127 - 128: 15.117 distance: 128 - 129: 6.878 distance: 129 - 130: 19.213 distance: 131 - 132: 6.644 distance: 132 - 133: 18.097 distance: 132 - 135: 16.071 distance: 133 - 134: 10.023 distance: 133 - 139: 14.681 distance: 135 - 136: 9.939 distance: 135 - 137: 10.092 distance: 136 - 138: 4.837 distance: 139 - 140: 6.170 distance: 140 - 141: 8.575 distance: 140 - 143: 6.648 distance: 141 - 142: 17.581 distance: 141 - 145: 3.495 distance: 143 - 144: 21.104