Starting phenix.real_space_refine on Fri Aug 22 13:46:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qw4_18680/08_2025/8qw4_18680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qw4_18680/08_2025/8qw4_18680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qw4_18680/08_2025/8qw4_18680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qw4_18680/08_2025/8qw4_18680.map" model { file = "/net/cci-nas-00/data/ceres_data/8qw4_18680/08_2025/8qw4_18680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qw4_18680/08_2025/8qw4_18680.cif" } resolution = 2.9 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= 0.019 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 27 5.16 5 C 2286 2.51 5 N 564 2.21 5 O 602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s 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: 3479 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2591 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 4 Chain: "B" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 888 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Time building chain proxies: 1.13, per 1000 atoms: 0.32 Number of scatterers: 3479 At special positions: 0 Unit cell: (93.072, 57.339, 101.382, 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 27 16.00 O 602 8.00 N 564 7.00 C 2286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 264 " distance=2.04 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 98 " distance=2.02 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: 0.18 Conformation dependent library (CDL) restraints added in 82.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 808 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 52.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 195 through 225 removed outlier: 3.885A pdb=" N LEU A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 253 removed outlier: 3.963A pdb=" N PHE A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 283 through 313 removed outlier: 3.615A pdb=" N THR A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 290 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 291 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 327 through 345 Proline residue: A 339 - end of helix Processing helix chain 'A' and resid 367 through 375 removed outlier: 3.625A pdb=" N LEU A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 402 removed outlier: 4.147A pdb=" N SER A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 413 through 443 removed outlier: 4.077A pdb=" N PHE A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 445 through 452 removed outlier: 3.647A pdb=" N TRP A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 451 " --> pdb=" O GLY A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.533A pdb=" N LEU A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 removed outlier: 3.598A pdb=" N TYR A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 493 Proline residue: A 493 - end of helix No H-bonds generated for 'chain 'A' and resid 490 through 493' Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'B' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.357A pdb=" N TYR A 177 " --> pdb=" O CYS A 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 27 removed outlier: 4.382A pdb=" N ASP B 79 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.821A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP B 53 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET B 37 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 36 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 94 through 95 156 hydrogen bonds defined for protein. 438 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: 0.62 Time building geometry restraints manager: 0.27 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: 1034 1.34 - 1.46: 921 1.46 - 1.59: 1564 1.59 - 1.71: 0 1.71 - 1.83: 41 Bond restraints: 3560 Sorted by residual: bond pdb=" N GLU A 407 " pdb=" CA GLU A 407 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.50e-02 4.44e+03 2.99e+00 bond pdb=" C ASP A 476 " pdb=" N LEU A 477 " ideal model delta sigma weight residual 1.331 1.307 0.024 1.40e-02 5.10e+03 2.97e+00 bond pdb=" C LEU A 406 " pdb=" N GLU A 407 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.28e-02 6.10e+03 2.77e+00 bond pdb=" CB THR A 276 " pdb=" CG2 THR A 276 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.63e+00 bond pdb=" CB TYR A 177 " pdb=" CG TYR A 177 " ideal model delta sigma weight residual 1.512 1.477 0.035 2.20e-02 2.07e+03 2.48e+00 ... (remaining 3555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 4614 2.38 - 4.76: 169 4.76 - 7.14: 31 7.14 - 9.52: 5 9.52 - 11.91: 3 Bond angle restraints: 4822 Sorted by residual: angle pdb=" C GLU A 235 " pdb=" N ARG A 236 " pdb=" CA ARG A 236 " ideal model delta sigma weight residual 120.09 125.89 -5.80 1.25e+00 6.40e-01 2.15e+01 angle pdb=" N ARG A 459 " pdb=" CA ARG A 459 " pdb=" C ARG A 459 " ideal model delta sigma weight residual 110.80 101.02 9.78 2.13e+00 2.20e-01 2.11e+01 angle pdb=" N GLY A 354 " pdb=" CA GLY A 354 " pdb=" C GLY A 354 " ideal model delta sigma weight residual 112.13 118.02 -5.89 1.34e+00 5.57e-01 1.93e+01 angle pdb=" C ALA B 43 " pdb=" N PRO B 44 " pdb=" CA PRO B 44 " ideal model delta sigma weight residual 127.00 136.73 -9.73 2.40e+00 1.74e-01 1.64e+01 angle pdb=" C CYS A 458 " pdb=" N ARG A 459 " pdb=" CA ARG A 459 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 ... (remaining 4817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 1877 16.29 - 32.57: 177 32.57 - 48.86: 30 48.86 - 65.14: 4 65.14 - 81.43: 6 Dihedral angle restraints: 2094 sinusoidal: 837 harmonic: 1257 Sorted by residual: dihedral pdb=" CB CYS A 189 " pdb=" SG CYS A 189 " pdb=" SG CYS A 264 " pdb=" CB CYS A 264 " ideal model delta sinusoidal sigma weight residual -86.00 -157.10 71.10 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CA TYR A 177 " pdb=" C TYR A 177 " pdb=" N SER A 178 " pdb=" CA SER A 178 " ideal model delta harmonic sigma weight residual -180.00 -145.73 -34.27 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" CA SER A 178 " pdb=" C SER A 178 " pdb=" N PHE A 179 " pdb=" CA PHE A 179 " ideal model delta harmonic sigma weight residual -180.00 -146.92 -33.08 0 5.00e+00 4.00e-02 4.38e+01 ... (remaining 2091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 361 0.048 - 0.096: 136 0.096 - 0.144: 34 0.144 - 0.192: 17 0.192 - 0.241: 2 Chirality restraints: 550 Sorted by residual: chirality pdb=" CA VAL A 316 " pdb=" N VAL A 316 " pdb=" C VAL A 316 " pdb=" CB VAL A 316 " both_signs ideal model delta sigma weight residual False 2.44 2.20 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA PRO B 90 " pdb=" N PRO B 90 " pdb=" C PRO B 90 " pdb=" CB PRO B 90 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO A 405 " pdb=" N PRO A 405 " pdb=" C PRO A 405 " pdb=" CB PRO A 405 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.11e-01 ... (remaining 547 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 316 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO A 317 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 474 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO A 475 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 428 " 0.010 2.00e-02 2.50e+03 1.41e-02 3.99e+00 pdb=" CG TYR A 428 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 428 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 428 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 428 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 428 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 428 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 428 " -0.001 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 75 2.65 - 3.21: 3457 3.21 - 3.78: 5258 3.78 - 4.34: 7053 4.34 - 4.90: 11275 Nonbonded interactions: 27118 Sorted by model distance: nonbonded pdb=" O GLN A 455 " pdb=" NH2 ARG A 459 " model vdw 2.091 3.120 nonbonded pdb=" OH TYR A 241 " pdb=" O VAL A 490 " model vdw 2.209 3.040 nonbonded pdb=" O ASN A 410 " pdb=" N LYS A 413 " model vdw 2.275 3.120 nonbonded pdb=" O ASP A 260 " pdb=" NH1 ARG A 261 " model vdw 2.288 3.120 nonbonded pdb=" O THR A 217 " pdb=" OG1 THR A 220 " model vdw 2.300 3.040 ... (remaining 27113 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.340 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.210 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 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 0.057 3564 Z= 0.338 Angle : 1.104 11.906 4830 Z= 0.610 Chirality : 0.058 0.241 550 Planarity : 0.008 0.116 587 Dihedral : 13.197 81.429 1274 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 0.26 % Allowed : 0.00 % Favored : 99.74 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.29 (0.39), residues: 420 helix: -0.99 (0.37), residues: 189 sheet: -1.69 (0.86), residues: 38 loop : -3.62 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 41 TYR 0.034 0.003 TYR A 428 PHE 0.020 0.003 PHE A 201 TRP 0.013 0.002 TRP B 104 HIS 0.003 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00748 ( 3560) covalent geometry : angle 1.09835 ( 4822) SS BOND : bond 0.00704 ( 4) SS BOND : angle 3.02074 ( 8) hydrogen bonds : bond 0.16799 ( 156) hydrogen bonds : angle 6.60400 ( 438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6980 (tpt90) cc_final: 0.5436 (mtp180) REVERT: A 336 TRP cc_start: 0.7890 (m100) cc_final: 0.7653 (m-10) REVERT: A 349 MET cc_start: 0.4417 (mmt) cc_final: 0.3585 (ptt) REVERT: A 442 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6693 (mp0) REVERT: B 35 ASP cc_start: 0.7720 (m-30) cc_final: 0.7504 (m-30) REVERT: B 55 THR cc_start: 0.7761 (p) cc_final: 0.7497 (m) outliers start: 1 outliers final: 2 residues processed: 119 average time/residue: 0.4648 time to fit residues: 57.2742 Evaluate side-chains 67 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 352 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.186725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.171095 restraints weight = 8096.791| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 3.58 r_work: 0.4278 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3564 Z= 0.173 Angle : 0.862 8.097 4830 Z= 0.438 Chirality : 0.049 0.188 550 Planarity : 0.007 0.069 587 Dihedral : 7.291 36.516 478 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.75 % Allowed : 17.94 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.79 (0.39), residues: 420 helix: -0.69 (0.38), residues: 188 sheet: -1.03 (0.85), residues: 38 loop : -3.31 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 372 TYR 0.016 0.002 TYR A 445 PHE 0.025 0.002 PHE B 32 TRP 0.014 0.002 TRP A 449 HIS 0.001 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 3560) covalent geometry : angle 0.86171 ( 4822) SS BOND : bond 0.00230 ( 4) SS BOND : angle 1.16149 ( 8) hydrogen bonds : bond 0.05012 ( 156) hydrogen bonds : angle 5.33947 ( 438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.156 Fit side-chains REVERT: A 203 ARG cc_start: 0.6683 (tpt90) cc_final: 0.5183 (mtp180) REVERT: A 291 MET cc_start: 0.6511 (ptt) cc_final: 0.6225 (pmm) REVERT: A 336 TRP cc_start: 0.8470 (m100) cc_final: 0.7681 (m-10) REVERT: A 349 MET cc_start: 0.4920 (mmt) cc_final: 0.3455 (ptt) REVERT: A 367 ASP cc_start: 0.7844 (t0) cc_final: 0.7539 (t0) REVERT: A 415 VAL cc_start: 0.5976 (OUTLIER) cc_final: 0.4867 (t) REVERT: A 445 TYR cc_start: 0.6674 (t80) cc_final: 0.6394 (t80) REVERT: B 35 ASP cc_start: 0.8701 (m-30) cc_final: 0.8437 (m-30) REVERT: B 109 TYR cc_start: 0.7746 (m-80) cc_final: 0.7360 (m-80) outliers start: 18 outliers final: 5 residues processed: 83 average time/residue: 0.5060 time to fit residues: 43.4606 Evaluate side-chains 73 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 33 optimal weight: 0.0270 chunk 8 optimal weight: 0.4980 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.187631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.171893 restraints weight = 8071.926| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 3.71 r_work: 0.4284 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3564 Z= 0.156 Angle : 0.797 8.294 4830 Z= 0.405 Chirality : 0.048 0.284 550 Planarity : 0.006 0.059 587 Dihedral : 6.731 34.580 476 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 3.69 % Allowed : 22.43 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.60 (0.40), residues: 420 helix: -0.46 (0.38), residues: 189 sheet: -1.05 (0.82), residues: 36 loop : -3.26 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 183 TYR 0.019 0.002 TYR A 428 PHE 0.021 0.002 PHE B 32 TRP 0.022 0.001 TRP A 449 HIS 0.001 0.000 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 3560) covalent geometry : angle 0.79687 ( 4822) SS BOND : bond 0.00200 ( 4) SS BOND : angle 0.83268 ( 8) hydrogen bonds : bond 0.04489 ( 156) hydrogen bonds : angle 5.11736 ( 438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6640 (tpt90) cc_final: 0.5214 (tpt-90) REVERT: A 243 VAL cc_start: 0.8885 (m) cc_final: 0.8684 (p) REVERT: A 336 TRP cc_start: 0.8359 (m100) cc_final: 0.7572 (m-10) REVERT: A 349 MET cc_start: 0.4820 (mmt) cc_final: 0.3420 (ptt) REVERT: A 367 ASP cc_start: 0.7697 (t0) cc_final: 0.7222 (t0) REVERT: A 415 VAL cc_start: 0.5817 (OUTLIER) cc_final: 0.4639 (t) REVERT: A 433 LEU cc_start: 0.8154 (tm) cc_final: 0.7648 (pp) REVERT: A 480 PHE cc_start: 0.7968 (m-10) cc_final: 0.7656 (m-80) REVERT: B 35 ASP cc_start: 0.8856 (m-30) cc_final: 0.8550 (m-30) REVERT: B 109 TYR cc_start: 0.7784 (m-80) cc_final: 0.7470 (m-80) outliers start: 14 outliers final: 4 residues processed: 86 average time/residue: 0.4330 time to fit residues: 38.6299 Evaluate side-chains 66 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.0470 chunk 38 optimal weight: 0.0980 overall best weight: 0.3278 ------------------------------------------------------------------------------- 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 = 0.4545 r_free = 0.4545 target = 0.187784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.172852 restraints weight = 8175.727| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 3.53 r_work: 0.4294 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3564 Z= 0.149 Angle : 0.789 9.541 4830 Z= 0.391 Chirality : 0.046 0.179 550 Planarity : 0.005 0.059 587 Dihedral : 6.236 24.730 473 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 5.28 % Allowed : 25.59 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.34 (0.40), residues: 420 helix: -0.28 (0.38), residues: 189 sheet: -0.82 (0.85), residues: 36 loop : -3.09 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 183 TYR 0.022 0.002 TYR A 428 PHE 0.016 0.002 PHE B 32 TRP 0.012 0.001 TRP A 449 HIS 0.001 0.000 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 3560) covalent geometry : angle 0.78927 ( 4822) SS BOND : bond 0.00182 ( 4) SS BOND : angle 0.61060 ( 8) hydrogen bonds : bond 0.04267 ( 156) hydrogen bonds : angle 4.97917 ( 438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6638 (tpt90) cc_final: 0.5198 (tpt-90) REVERT: A 349 MET cc_start: 0.4796 (mmt) cc_final: 0.3735 (ptt) REVERT: A 415 VAL cc_start: 0.5727 (OUTLIER) cc_final: 0.4443 (t) REVERT: A 433 LEU cc_start: 0.8331 (tm) cc_final: 0.7779 (pp) REVERT: A 445 TYR cc_start: 0.6448 (t80) cc_final: 0.6183 (t80) REVERT: A 482 MET cc_start: 0.7152 (pp-130) cc_final: 0.6940 (mtt) REVERT: B 35 ASP cc_start: 0.8806 (m-30) cc_final: 0.8510 (m-30) REVERT: B 109 TYR cc_start: 0.7775 (m-80) cc_final: 0.7477 (m-80) outliers start: 20 outliers final: 7 residues processed: 85 average time/residue: 0.4150 time to fit residues: 36.7133 Evaluate side-chains 72 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 52.7495 > 50: distance: 62 - 82: 19.411 distance: 65 - 79: 28.037 distance: 73 - 79: 28.535 distance: 79 - 80: 20.292 distance: 80 - 81: 16.654 distance: 80 - 83: 19.309 distance: 81 - 82: 16.129 distance: 81 - 88: 14.037 distance: 83 - 84: 20.502 distance: 84 - 85: 26.176 distance: 85 - 86: 20.800 distance: 85 - 87: 15.107 distance: 88 - 89: 17.284 distance: 89 - 90: 19.851 distance: 89 - 92: 17.194 distance: 90 - 91: 30.200 distance: 90 - 96: 15.941 distance: 92 - 93: 23.264 distance: 93 - 94: 8.202 distance: 94 - 95: 18.634 distance: 96 - 97: 7.668 distance: 97 - 98: 20.488 distance: 97 - 100: 15.283 distance: 98 - 99: 27.081 distance: 98 - 104: 21.294 distance: 100 - 101: 11.753 distance: 101 - 102: 8.116 distance: 101 - 103: 7.746 distance: 104 - 105: 9.384 distance: 105 - 106: 5.936 distance: 105 - 108: 8.533 distance: 106 - 107: 13.355 distance: 106 - 110: 20.136 distance: 108 - 109: 8.774 distance: 111 - 112: 3.659 distance: 111 - 114: 22.122 distance: 112 - 113: 15.495 distance: 112 - 118: 14.825 distance: 114 - 115: 31.155 distance: 115 - 116: 12.709 distance: 115 - 117: 18.595 distance: 118 - 119: 11.703 distance: 119 - 120: 11.692 distance: 119 - 122: 5.866 distance: 120 - 121: 35.720 distance: 120 - 127: 34.375 distance: 121 - 143: 15.668 distance: 122 - 123: 11.746 distance: 123 - 124: 18.669 distance: 124 - 125: 29.534 distance: 125 - 126: 27.060 distance: 127 - 128: 26.886 distance: 127 - 133: 14.898 distance: 128 - 129: 18.768 distance: 128 - 131: 26.090 distance: 129 - 130: 18.226 distance: 129 - 134: 22.995 distance: 130 - 151: 23.406 distance: 131 - 132: 19.157 distance: 132 - 133: 14.700 distance: 134 - 135: 35.005 distance: 135 - 136: 20.466 distance: 135 - 138: 12.149 distance: 136 - 137: 25.137 distance: 136 - 143: 29.150 distance: 138 - 139: 11.754 distance: 139 - 140: 9.269 distance: 140 - 141: 11.118 distance: 140 - 142: 13.427 distance: 143 - 144: 22.722 distance: 144 - 145: 14.015 distance: 144 - 147: 28.808 distance: 145 - 146: 24.678 distance: 145 - 151: 29.592 distance: 147 - 148: 19.033 distance: 148 - 149: 34.535 distance: 148 - 150: 31.886 distance: 151 - 152: 29.462 distance: 152 - 153: 28.607 distance: 152 - 155: 24.415 distance: 153 - 154: 22.164 distance: 153 - 158: 16.677 distance: 155 - 156: 11.021 distance: 155 - 157: 6.594