Starting phenix.real_space_refine on Thu Jul 18 17:37:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x63_38078/07_2024/8x63_38078.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x63_38078/07_2024/8x63_38078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x63_38078/07_2024/8x63_38078.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x63_38078/07_2024/8x63_38078.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x63_38078/07_2024/8x63_38078.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x63_38078/07_2024/8x63_38078.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 1509 2.51 5 N 366 2.21 5 O 357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2252 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2231 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 2 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'Y5E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.21, per 1000 atoms: 0.98 Number of scatterers: 2252 At special positions: 0 Unit cell: (50.29, 75.97, 71.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 357 8.00 N 366 7.00 C 1509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 444 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 418.8 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 524 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 86.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 27 through 55 removed outlier: 3.715A pdb=" N VAL B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 36 " --> pdb=" O VAL B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 90 Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 96 through 129 removed outlier: 3.537A pdb=" N CYS B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 164 Proline residue: B 161 - end of helix removed outlier: 3.908A pdb=" N GLY B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 186 removed outlier: 3.534A pdb=" N TYR B 185 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP B 186 " --> pdb=" O ASP B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 186' Processing helix chain 'B' and resid 187 through 221 removed outlier: 3.949A pdb=" N LYS B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 409 through 427 Processing helix chain 'B' and resid 428 through 441 removed outlier: 3.521A pdb=" N ALA B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE B 440 " --> pdb=" O MET B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 445 removed outlier: 3.832A pdb=" N CYS B 445 " --> pdb=" O LYS B 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 442 through 445' Processing helix chain 'B' and resid 446 through 472 Proline residue: B 465 - end of helix Proline residue: B 469 - end of helix removed outlier: 4.076A pdb=" N ASN B 472 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 481 removed outlier: 4.135A pdb=" N LYS B 476 " --> pdb=" O ASN B 472 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) 161 hydrogen bonds defined for protein. 483 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: 0.54 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 314 1.29 - 1.42: 669 1.42 - 1.55: 1299 1.55 - 1.68: 2 1.68 - 1.81: 31 Bond restraints: 2315 Sorted by residual: bond pdb=" C PHE B 424 " pdb=" N ILE B 425 " ideal model delta sigma weight residual 1.331 1.246 0.085 1.42e-02 4.96e+03 3.60e+01 bond pdb=" C ILE B 115 " pdb=" O ILE B 115 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.19e-02 7.06e+03 3.09e+01 bond pdb=" C14 Y5E B 601 " pdb=" N08 Y5E B 601 " ideal model delta sigma weight residual 1.368 1.477 -0.109 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C PHE B 424 " pdb=" O PHE B 424 " ideal model delta sigma weight residual 1.236 1.160 0.076 1.47e-02 4.63e+03 2.65e+01 bond pdb=" N PHE B 424 " pdb=" CA PHE B 424 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.40e-02 5.10e+03 1.40e+01 ... (remaining 2310 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.26: 40 105.26 - 112.45: 1186 112.45 - 119.64: 779 119.64 - 126.83: 1092 126.83 - 134.03: 43 Bond angle restraints: 3140 Sorted by residual: angle pdb=" C PHE B 424 " pdb=" N ILE B 425 " pdb=" CA ILE B 425 " ideal model delta sigma weight residual 122.97 116.24 6.73 9.80e-01 1.04e+00 4.71e+01 angle pdb=" N VAL B 129 " pdb=" CA VAL B 129 " pdb=" C VAL B 129 " ideal model delta sigma weight residual 111.77 105.86 5.91 1.04e+00 9.25e-01 3.23e+01 angle pdb=" O ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 122.07 116.28 5.79 1.03e+00 9.43e-01 3.16e+01 angle pdb=" CA ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 117.07 122.70 -5.63 1.14e+00 7.69e-01 2.44e+01 angle pdb=" O SER B 114 " pdb=" C SER B 114 " pdb=" N ILE B 115 " ideal model delta sigma weight residual 122.03 116.85 5.18 1.08e+00 8.57e-01 2.30e+01 ... (remaining 3135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 1183 16.56 - 33.12: 136 33.12 - 49.68: 32 49.68 - 66.24: 6 66.24 - 82.80: 3 Dihedral angle restraints: 1360 sinusoidal: 555 harmonic: 805 Sorted by residual: dihedral pdb=" N PHE B 424 " pdb=" C PHE B 424 " pdb=" CA PHE B 424 " pdb=" CB PHE B 424 " ideal model delta harmonic sigma weight residual 122.80 135.14 -12.34 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" C PHE B 424 " pdb=" N PHE B 424 " pdb=" CA PHE B 424 " pdb=" CB PHE B 424 " ideal model delta harmonic sigma weight residual -122.60 -134.83 12.23 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" CA ILE B 115 " pdb=" C ILE B 115 " pdb=" N PHE B 116 " pdb=" CA PHE B 116 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 1357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 346 0.098 - 0.196: 9 0.196 - 0.293: 0 0.293 - 0.391: 0 0.391 - 0.488: 2 Chirality restraints: 357 Sorted by residual: chirality pdb=" CA PHE B 424 " pdb=" N PHE B 424 " pdb=" C PHE B 424 " pdb=" CB PHE B 424 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" CA ILE B 115 " pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CB ILE B 115 " both_signs ideal model delta sigma weight residual False 2.43 2.02 0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA VAL B 129 " pdb=" N VAL B 129 " pdb=" C VAL B 129 " pdb=" CB VAL B 129 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 354 not shown) Planarity restraints: 371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 424 " 0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C PHE B 424 " -0.079 2.00e-02 2.50e+03 pdb=" O PHE B 424 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE B 425 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " -0.019 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C SER B 114 " 0.062 2.00e-02 2.50e+03 pdb=" O SER B 114 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE B 115 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 115 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C ILE B 115 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE B 115 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE B 116 " 0.021 2.00e-02 2.50e+03 ... (remaining 368 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 881 2.91 - 3.41: 2385 3.41 - 3.90: 3516 3.90 - 4.40: 3884 4.40 - 4.90: 6390 Nonbonded interactions: 17056 Sorted by model distance: nonbonded pdb=" O PHE B 424 " pdb=" CG PHE B 424 " model vdw 2.411 3.260 nonbonded pdb=" O ASN B 408 " pdb=" N ARG B 411 " model vdw 2.513 2.520 nonbonded pdb=" O HIS B 450 " pdb=" OG1 THR B 453 " model vdw 2.516 2.440 nonbonded pdb=" O PHE B 424 " pdb=" CD1 PHE B 424 " model vdw 2.519 3.340 nonbonded pdb=" CG2 ILE B 115 " pdb=" CD1 ILE B 115 " model vdw 2.520 3.104 ... (remaining 17051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.360 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1172 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 : 0.006 0.109 2315 Z= 0.372 Angle : 0.773 7.099 3140 Z= 0.459 Chirality : 0.055 0.488 357 Planarity : 0.007 0.051 371 Dihedral : 15.286 82.798 830 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.81 % Allowed : 0.41 % Favored : 98.78 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.52), residues: 264 helix: 1.06 (0.37), residues: 196 sheet: None (None), residues: 0 loop : -3.58 (0.62), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 165 HIS 0.009 0.002 HIS B 59 PHE 0.027 0.002 PHE B 435 TYR 0.011 0.001 TYR B 214 ARG 0.007 0.001 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.228 Fit side-chains REVERT: B 45 ASN cc_start: 0.2777 (m-40) cc_final: 0.2053 (m110) outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.1327 time to fit residues: 4.4426 Evaluate side-chains 18 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.0370 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2645 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 2315 Z= 0.327 Angle : 0.885 9.873 3140 Z= 0.449 Chirality : 0.048 0.158 357 Planarity : 0.007 0.060 371 Dihedral : 5.772 29.463 308 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.81 % Allowed : 11.38 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.49), residues: 264 helix: 0.47 (0.34), residues: 210 sheet: None (None), residues: 0 loop : -4.48 (0.61), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP B 93 HIS 0.003 0.001 HIS B 167 PHE 0.012 0.002 PHE B 102 TYR 0.013 0.002 TYR B 87 ARG 0.004 0.001 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: B 56 ARG cc_start: 0.1105 (mmt90) cc_final: 0.0843 (tpp80) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.1372 time to fit residues: 4.1650 Evaluate side-chains 21 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.0470 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3290 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2315 Z= 0.252 Angle : 0.754 10.107 3140 Z= 0.381 Chirality : 0.044 0.182 357 Planarity : 0.006 0.047 371 Dihedral : 6.432 37.890 306 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.44 % Allowed : 16.26 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.52), residues: 264 helix: 0.81 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -4.60 (0.60), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP B 93 HIS 0.006 0.001 HIS B 59 PHE 0.011 0.001 PHE B 432 TYR 0.013 0.002 TYR B 468 ARG 0.004 0.001 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: B 56 ARG cc_start: 0.2853 (mmt90) cc_final: 0.1683 (tpt170) REVERT: B 451 MET cc_start: 0.3946 (ptp) cc_final: 0.1997 (mmp) outliers start: 6 outliers final: 4 residues processed: 26 average time/residue: 0.1207 time to fit residues: 3.9809 Evaluate side-chains 22 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 106 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4767 moved from start: 1.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 2315 Z= 0.404 Angle : 0.948 7.772 3140 Z= 0.508 Chirality : 0.054 0.161 357 Planarity : 0.007 0.064 371 Dihedral : 6.545 27.574 306 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.88 % Allowed : 21.54 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.48), residues: 264 helix: -0.36 (0.34), residues: 210 sheet: None (None), residues: 0 loop : -4.33 (0.67), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP B 455 HIS 0.008 0.003 HIS B 59 PHE 0.022 0.002 PHE B 432 TYR 0.017 0.003 TYR B 431 ARG 0.007 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 0.249 Fit side-chains REVERT: B 171 GLN cc_start: 0.4664 (mt0) cc_final: 0.4309 (mm-40) REVERT: B 432 PHE cc_start: 0.5758 (OUTLIER) cc_final: 0.4213 (t80) outliers start: 12 outliers final: 8 residues processed: 40 average time/residue: 0.1187 time to fit residues: 5.8927 Evaluate side-chains 34 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.0870 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5029 moved from start: 1.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 2315 Z= 0.283 Angle : 0.806 10.276 3140 Z= 0.411 Chirality : 0.046 0.136 357 Planarity : 0.006 0.049 371 Dihedral : 6.315 27.082 306 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.07 % Allowed : 25.20 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.51), residues: 264 helix: 0.34 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -4.18 (0.61), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 93 HIS 0.009 0.002 HIS B 59 PHE 0.007 0.001 PHE B 199 TYR 0.011 0.002 TYR B 138 ARG 0.004 0.001 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 27 time to evaluate : 0.188 Fit side-chains REVERT: B 193 MET cc_start: 0.5981 (ttm) cc_final: 0.5673 (mtt) outliers start: 10 outliers final: 6 residues processed: 35 average time/residue: 0.0986 time to fit residues: 4.3793 Evaluate side-chains 29 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 454 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.0470 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 16 optimal weight: 0.0570 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5064 moved from start: 1.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2315 Z= 0.204 Angle : 0.702 6.542 3140 Z= 0.359 Chirality : 0.043 0.140 357 Planarity : 0.005 0.041 371 Dihedral : 5.644 24.789 306 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.85 % Allowed : 28.05 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.53), residues: 264 helix: 0.85 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -4.17 (0.58), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 93 HIS 0.005 0.001 HIS B 59 PHE 0.014 0.001 PHE B 432 TYR 0.007 0.001 TYR B 138 ARG 0.002 0.000 ARG B 411 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.178 Fit side-chains REVERT: B 193 MET cc_start: 0.5972 (ttm) cc_final: 0.5663 (mtt) REVERT: B 451 MET cc_start: 0.3845 (OUTLIER) cc_final: 0.3364 (mmm) outliers start: 7 outliers final: 2 residues processed: 28 average time/residue: 0.1034 time to fit residues: 3.6573 Evaluate side-chains 25 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 451 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.0270 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.0070 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5410 moved from start: 1.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2315 Z= 0.265 Angle : 0.817 9.566 3140 Z= 0.415 Chirality : 0.045 0.173 357 Planarity : 0.005 0.037 371 Dihedral : 5.959 24.477 306 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.66 % Allowed : 25.61 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.51), residues: 264 helix: 0.71 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -4.62 (0.51), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 93 HIS 0.013 0.003 HIS B 59 PHE 0.013 0.001 PHE B 432 TYR 0.013 0.002 TYR B 138 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 23 time to evaluate : 0.180 Fit side-chains REVERT: B 83 MET cc_start: 0.3063 (tmm) cc_final: 0.2324 (mtt) REVERT: B 193 MET cc_start: 0.6271 (ttm) cc_final: 0.5964 (mtt) outliers start: 9 outliers final: 6 residues processed: 30 average time/residue: 0.1248 time to fit residues: 4.7009 Evaluate side-chains 26 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.3553 > 50: distance: 10 - 31: 3.292 distance: 14 - 40: 15.935 distance: 18 - 45: 17.660 distance: 22 - 31: 6.802 distance: 23 - 52: 20.279 distance: 31 - 32: 3.471 distance: 32 - 33: 5.817 distance: 32 - 35: 23.564 distance: 33 - 34: 22.354 distance: 33 - 40: 21.177 distance: 34 - 61: 44.162 distance: 35 - 36: 16.358 distance: 36 - 37: 7.538 distance: 37 - 38: 16.610 distance: 38 - 39: 28.046 distance: 40 - 41: 7.737 distance: 41 - 42: 14.386 distance: 41 - 44: 13.112 distance: 42 - 43: 11.487 distance: 42 - 45: 11.902 distance: 43 - 72: 20.373 distance: 45 - 46: 18.455 distance: 46 - 47: 12.058 distance: 46 - 49: 22.556 distance: 47 - 48: 9.852 distance: 47 - 52: 33.317 distance: 48 - 81: 30.932 distance: 49 - 50: 26.938 distance: 49 - 51: 29.445 distance: 52 - 53: 4.841 distance: 53 - 54: 12.324 distance: 53 - 56: 25.597 distance: 54 - 55: 9.485 distance: 54 - 61: 8.108 distance: 56 - 57: 7.624 distance: 57 - 58: 23.178 distance: 58 - 59: 18.308 distance: 59 - 60: 30.453 distance: 61 - 62: 12.399 distance: 62 - 63: 16.625 distance: 62 - 65: 17.900 distance: 63 - 72: 33.456 distance: 65 - 66: 28.730 distance: 66 - 67: 12.374 distance: 67 - 68: 10.963 distance: 69 - 70: 6.157 distance: 72 - 73: 7.832 distance: 73 - 74: 15.148 distance: 73 - 76: 10.376 distance: 74 - 75: 13.780 distance: 74 - 81: 38.676 distance: 76 - 77: 16.080 distance: 77 - 78: 6.948 distance: 78 - 79: 13.405 distance: 78 - 80: 21.473 distance: 81 - 82: 15.501 distance: 82 - 83: 15.493 distance: 82 - 85: 7.640 distance: 83 - 84: 14.581 distance: 85 - 86: 10.227 distance: 86 - 87: 15.162 distance: 86 - 88: 12.088 distance: 89 - 90: 6.961 distance: 90 - 91: 19.069 distance: 90 - 93: 8.089 distance: 91 - 92: 17.368 distance: 91 - 97: 21.545 distance: 93 - 94: 7.975 distance: 94 - 95: 13.531 distance: 94 - 96: 10.629 distance: 97 - 98: 12.971 distance: 98 - 99: 19.926 distance: 98 - 101: 18.906 distance: 99 - 100: 6.219 distance: 100 - 135: 19.232 distance: 101 - 102: 4.025 distance: 102 - 103: 14.917 distance: 103 - 104: 15.655 distance: 104 - 105: 14.578 distance: 105 - 106: 16.488 distance: 105 - 107: 17.102 distance: 108 - 109: 8.880 distance: 109 - 110: 11.850 distance: 109 - 112: 5.506 distance: 110 - 111: 3.090 distance: 110 - 117: 5.625 distance: 111 - 140: 11.962 distance: 112 - 113: 15.437 distance: 113 - 114: 8.954 distance: 114 - 115: 12.618 distance: 114 - 116: 13.882