Starting phenix.real_space_refine on Sun Apr 27 05:28:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7the_25893/04_2025/7the_25893.cif Found real_map, /net/cci-nas-00/data/ceres_data/7the_25893/04_2025/7the_25893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7the_25893/04_2025/7the_25893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7the_25893/04_2025/7the_25893.map" model { file = "/net/cci-nas-00/data/ceres_data/7the_25893/04_2025/7the_25893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7the_25893/04_2025/7the_25893.cif" } resolution = 3.87 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= -0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1543 atoms to isotropic. 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 17 5.16 5 C 2098 2.51 5 N 549 2.21 5 O 641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3305 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "B" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "C" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.97, per 1000 atoms: 0.90 Number of scatterers: 3305 At special positions: 0 Unit cell: (65.596, 81.466, 87.814, 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 17 16.00 O 641 8.00 N 549 7.00 C 2098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.01 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " 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=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 412.9 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 12.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.981A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.706A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.854A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'C' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 334 through 335 removed outlier: 7.513A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.975A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.378A pdb=" N GLU B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 34 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.378A pdb=" N GLU B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B 102 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.730A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) 109 hydrogen bonds defined for protein. 252 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: 0.93 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 928 1.33 - 1.45: 657 1.45 - 1.57: 1781 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 3388 Sorted by residual: bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.482 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" CZ ARG B 94 " pdb=" NH2 ARG B 94 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.10e+01 bond pdb=" CZ ARG A 509 " pdb=" NH2 ARG A 509 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" CZ ARG A 457 " pdb=" NH2 ARG A 457 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" CZ ARG A 357 " pdb=" NH2 ARG A 357 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.02e+01 ... (remaining 3383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 3171 1.82 - 3.63: 1161 3.63 - 5.45: 247 5.45 - 7.26: 22 7.26 - 9.08: 4 Bond angle restraints: 4605 Sorted by residual: angle pdb=" CA PHE A 347 " pdb=" CB PHE A 347 " pdb=" CG PHE A 347 " ideal model delta sigma weight residual 113.80 119.35 -5.55 1.00e+00 1.00e+00 3.08e+01 angle pdb=" N CYS A 361 " pdb=" CA CYS A 361 " pdb=" C CYS A 361 " ideal model delta sigma weight residual 108.79 117.19 -8.40 1.53e+00 4.27e-01 3.01e+01 angle pdb=" C THR A 393 " pdb=" N ASN A 394 " pdb=" CA ASN A 394 " ideal model delta sigma weight residual 121.75 130.83 -9.08 1.73e+00 3.34e-01 2.75e+01 angle pdb=" CA ASP A 405 " pdb=" CB ASP A 405 " pdb=" CG ASP A 405 " ideal model delta sigma weight residual 112.60 117.25 -4.65 1.00e+00 1.00e+00 2.16e+01 angle pdb=" CA ASP C 70 " pdb=" CB ASP C 70 " pdb=" CG ASP C 70 " ideal model delta sigma weight residual 112.60 117.16 -4.56 1.00e+00 1.00e+00 2.08e+01 ... (remaining 4600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 1841 16.95 - 33.89: 139 33.89 - 50.84: 30 50.84 - 67.79: 8 67.79 - 84.73: 4 Dihedral angle restraints: 2022 sinusoidal: 794 harmonic: 1228 Sorted by residual: dihedral pdb=" CA ARG B 83 " pdb=" C ARG B 83 " pdb=" N SER B 84 " pdb=" CA SER B 84 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA TYR B 32 " pdb=" C TYR B 32 " pdb=" N ALA B 33 " pdb=" CA ALA B 33 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA TYR B 91 " pdb=" C TYR B 91 " pdb=" N CYS B 92 " pdb=" CA CYS B 92 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 2019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 270 0.076 - 0.152: 164 0.152 - 0.228: 49 0.228 - 0.303: 10 0.303 - 0.379: 6 Chirality restraints: 499 Sorted by residual: chirality pdb=" CA ALA A 520 " pdb=" N ALA A 520 " pdb=" C ALA A 520 " pdb=" CB ALA A 520 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA ARG B 83 " pdb=" N ARG B 83 " pdb=" C ARG B 83 " pdb=" CB ARG B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA LEU A 455 " pdb=" N LEU A 455 " pdb=" C LEU A 455 " pdb=" CB LEU A 455 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 496 not shown) Planarity restraints: 595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 47 " -0.113 2.00e-02 2.50e+03 5.99e-02 8.96e+01 pdb=" CG TRP B 47 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP B 47 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 47 " 0.069 2.00e-02 2.50e+03 pdb=" NE1 TRP B 47 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP B 47 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 47 " 0.087 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 47 " -0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 47 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 47 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 103 " 0.104 2.00e-02 2.50e+03 5.15e-02 6.64e+01 pdb=" CG TRP B 103 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP B 103 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP B 103 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP B 103 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP B 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 103 " -0.070 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 103 " 0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 103 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP B 103 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 351 " 0.102 2.00e-02 2.50e+03 5.49e-02 6.03e+01 pdb=" CG TYR A 351 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 351 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR A 351 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 351 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 351 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR A 351 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 351 " 0.085 2.00e-02 2.50e+03 ... (remaining 592 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 1818 3.02 - 3.49: 3232 3.49 - 3.96: 5382 3.96 - 4.43: 5919 4.43 - 4.90: 9826 Nonbonded interactions: 26177 Sorted by model distance: nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.548 3.040 nonbonded pdb=" OD1 ASP A 467 " pdb=" OG SER A 469 " model vdw 2.565 3.040 nonbonded pdb=" OE2 GLU A 484 " pdb=" OH TYR B 95 " model vdw 2.566 3.040 nonbonded pdb=" OH TYR B 100B" pdb=" OD1 ASN C 34 " model vdw 2.569 3.040 nonbonded pdb=" OE2 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.588 3.040 ... (remaining 26172 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.520 Find NCS groups from input model: 0.030 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 : 0.013 0.069 3395 Z= 0.746 Angle : 1.878 9.080 4620 Z= 1.233 Chirality : 0.106 0.379 499 Planarity : 0.015 0.104 594 Dihedral : 13.764 84.731 1226 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.39), residues: 417 helix: -4.02 (0.48), residues: 40 sheet: 0.21 (0.50), residues: 117 loop : -1.70 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.029 TRP B 47 HIS 0.007 0.004 HIS A 519 PHE 0.062 0.013 PHE B 54 TYR 0.102 0.022 TYR A 351 ARG 0.015 0.002 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.01889 ( 1) link_NAG-ASN : angle 4.19601 ( 3) hydrogen bonds : bond 0.17838 ( 107) hydrogen bonds : angle 8.01727 ( 252) SS BOND : bond 0.01072 ( 6) SS BOND : angle 1.28223 ( 12) covalent geometry : bond 0.01303 ( 3388) covalent geometry : angle 1.87726 ( 4605) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7767 (p-90) cc_final: 0.7518 (p-90) REVERT: A 484 GLU cc_start: 0.8295 (pm20) cc_final: 0.7878 (pm20) REVERT: A 493 GLN cc_start: 0.8765 (tt0) cc_final: 0.8364 (tt0) REVERT: A 506 GLN cc_start: 0.7602 (mt0) cc_final: 0.7191 (mt0) REVERT: B 36 TRP cc_start: 0.9068 (m100) cc_final: 0.8253 (m-10) REVERT: B 48 MET cc_start: 0.8169 (mtp) cc_final: 0.7521 (mtm) REVERT: B 56 ILE cc_start: 0.8594 (mt) cc_final: 0.8365 (tt) REVERT: B 105 GLN cc_start: 0.8720 (tt0) cc_final: 0.8165 (pt0) REVERT: C 34 ASN cc_start: 0.8908 (m-40) cc_final: 0.7510 (m-40) REVERT: C 89 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7010 (tm-30) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2122 time to fit residues: 31.4106 Evaluate side-chains 90 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN B 58 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.115099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102719 restraints weight = 8826.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105617 restraints weight = 4609.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.107508 restraints weight = 2850.357| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3395 Z= 0.173 Angle : 0.726 6.328 4620 Z= 0.392 Chirality : 0.048 0.166 499 Planarity : 0.005 0.036 594 Dihedral : 7.512 55.944 489 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.05 % Allowed : 12.74 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.50 (0.39), residues: 417 helix: -3.35 (0.68), residues: 35 sheet: 0.09 (0.45), residues: 138 loop : -1.30 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.021 0.002 PHE C 98 TYR 0.020 0.002 TYR A 365 ARG 0.005 0.001 ARG B 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 1) link_NAG-ASN : angle 2.34070 ( 3) hydrogen bonds : bond 0.04116 ( 107) hydrogen bonds : angle 6.31171 ( 252) SS BOND : bond 0.00536 ( 6) SS BOND : angle 0.99854 ( 12) covalent geometry : bond 0.00381 ( 3388) covalent geometry : angle 0.72296 ( 4605) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7148 (ttp-110) REVERT: A 406 GLU cc_start: 0.8422 (pt0) cc_final: 0.7431 (pt0) REVERT: A 467 ASP cc_start: 0.7647 (t0) cc_final: 0.6459 (p0) REVERT: A 468 ILE cc_start: 0.9153 (pt) cc_final: 0.8925 (pt) REVERT: B 36 TRP cc_start: 0.9015 (m100) cc_final: 0.8095 (m-10) REVERT: B 48 MET cc_start: 0.8105 (mtp) cc_final: 0.7520 (mtm) REVERT: B 96 MET cc_start: 0.8112 (mtp) cc_final: 0.7793 (mmm) REVERT: B 105 GLN cc_start: 0.8720 (tt0) cc_final: 0.8145 (pt0) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 0.1795 time to fit residues: 22.2261 Evaluate side-chains 95 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 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 = 0.3668 r_free = 0.3668 target = 0.115483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.103304 restraints weight = 8575.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.106231 restraints weight = 4435.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108143 restraints weight = 2726.428| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3395 Z= 0.158 Angle : 0.654 7.092 4620 Z= 0.348 Chirality : 0.045 0.160 499 Planarity : 0.005 0.047 594 Dihedral : 6.953 55.895 489 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.60 % Allowed : 15.79 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.29 (0.40), residues: 417 helix: -3.03 (0.75), residues: 35 sheet: 0.02 (0.41), residues: 150 loop : -1.08 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.008 0.001 PHE A 464 TYR 0.014 0.002 TYR A 365 ARG 0.008 0.001 ARG B 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 1) link_NAG-ASN : angle 1.98175 ( 3) hydrogen bonds : bond 0.03776 ( 107) hydrogen bonds : angle 6.12081 ( 252) SS BOND : bond 0.00261 ( 6) SS BOND : angle 0.92090 ( 12) covalent geometry : bond 0.00353 ( 3388) covalent geometry : angle 0.65122 ( 4605) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7622 (m110) cc_final: 0.7218 (m110) REVERT: A 467 ASP cc_start: 0.7404 (t0) cc_final: 0.6587 (p0) REVERT: B 32 TYR cc_start: 0.8406 (m-10) cc_final: 0.7947 (m-10) REVERT: B 36 TRP cc_start: 0.9071 (m100) cc_final: 0.8208 (m-10) REVERT: B 48 MET cc_start: 0.8115 (mtp) cc_final: 0.7402 (mtm) REVERT: B 50 ARG cc_start: 0.8097 (ttp-170) cc_final: 0.7843 (ttp-110) REVERT: B 61 GLN cc_start: 0.8906 (pm20) cc_final: 0.8390 (pp30) REVERT: B 96 MET cc_start: 0.8288 (mtp) cc_final: 0.7986 (mmt) REVERT: B 105 GLN cc_start: 0.8705 (tt0) cc_final: 0.8258 (pt0) REVERT: C 89 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7441 (tm-30) outliers start: 13 outliers final: 11 residues processed: 104 average time/residue: 0.1869 time to fit residues: 23.1872 Evaluate side-chains 98 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 0.0020 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 55 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 = 0.3700 r_free = 0.3700 target = 0.117349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.105183 restraints weight = 8672.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108076 restraints weight = 4478.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.109981 restraints weight = 2756.331| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3395 Z= 0.126 Angle : 0.619 7.275 4620 Z= 0.328 Chirality : 0.044 0.156 499 Planarity : 0.005 0.045 594 Dihedral : 6.509 55.259 489 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.88 % Allowed : 17.45 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.95 (0.41), residues: 417 helix: -2.69 (0.74), residues: 41 sheet: 0.16 (0.41), residues: 152 loop : -0.72 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.006 0.001 PHE A 464 TYR 0.018 0.001 TYR A 451 ARG 0.008 0.001 ARG B 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 1) link_NAG-ASN : angle 1.62864 ( 3) hydrogen bonds : bond 0.03364 ( 107) hydrogen bonds : angle 5.95472 ( 252) SS BOND : bond 0.00215 ( 6) SS BOND : angle 0.86935 ( 12) covalent geometry : bond 0.00277 ( 3388) covalent geometry : angle 0.61694 ( 4605) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7679 (m110) cc_final: 0.7235 (m110) REVERT: A 406 GLU cc_start: 0.8508 (pt0) cc_final: 0.8278 (pt0) REVERT: A 423 TYR cc_start: 0.7683 (t80) cc_final: 0.7479 (t80) REVERT: A 467 ASP cc_start: 0.7252 (t0) cc_final: 0.6363 (p0) REVERT: A 484 GLU cc_start: 0.7762 (pm20) cc_final: 0.7323 (pm20) REVERT: B 36 TRP cc_start: 0.8978 (m100) cc_final: 0.8431 (m-10) REVERT: B 99 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8509 (tmm-80) REVERT: B 105 GLN cc_start: 0.8704 (tt0) cc_final: 0.8200 (pt0) REVERT: C 31 ASN cc_start: 0.7863 (m-40) cc_final: 0.7190 (t0) outliers start: 14 outliers final: 13 residues processed: 99 average time/residue: 0.1758 time to fit residues: 20.6553 Evaluate side-chains 98 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.8073 > 50: distance: 40 - 50: 25.000 distance: 50 - 51: 20.879 distance: 51 - 52: 34.674 distance: 51 - 54: 55.044 distance: 52 - 53: 11.780 distance: 52 - 55: 35.336 distance: 55 - 56: 32.647 distance: 56 - 57: 10.182 distance: 56 - 59: 10.414 distance: 57 - 58: 12.382 distance: 57 - 60: 3.627 distance: 60 - 61: 16.663 distance: 61 - 62: 24.279 distance: 61 - 64: 21.276 distance: 62 - 63: 25.449 distance: 62 - 66: 14.471 distance: 64 - 65: 5.903 distance: 66 - 67: 11.957 distance: 67 - 68: 25.917 distance: 67 - 70: 12.947 distance: 68 - 69: 21.016 distance: 68 - 72: 9.707 distance: 70 - 71: 10.193 distance: 72 - 73: 26.277 distance: 73 - 74: 4.841 distance: 73 - 76: 34.345 distance: 74 - 75: 9.854 distance: 74 - 80: 11.498 distance: 76 - 77: 28.601 distance: 77 - 78: 24.511 distance: 77 - 79: 30.128 distance: 80 - 81: 12.912 distance: 81 - 82: 17.376 distance: 81 - 84: 10.073 distance: 82 - 83: 15.711 distance: 82 - 89: 11.451 distance: 84 - 85: 32.570 distance: 85 - 86: 42.895 distance: 86 - 88: 9.146 distance: 89 - 90: 11.174 distance: 90 - 91: 3.593 distance: 90 - 93: 8.437 distance: 91 - 92: 10.569 distance: 91 - 95: 29.891 distance: 93 - 94: 8.223 distance: 95 - 96: 9.812 distance: 96 - 97: 9.183 distance: 97 - 98: 31.952 distance: 97 - 99: 9.248 distance: 99 - 100: 12.940 distance: 100 - 101: 9.134 distance: 100 - 103: 17.923 distance: 101 - 102: 18.351 distance: 101 - 106: 13.084 distance: 103 - 104: 14.880 distance: 103 - 105: 19.749 distance: 106 - 107: 38.560 distance: 106 - 112: 20.065 distance: 107 - 108: 24.499 distance: 107 - 110: 41.397 distance: 108 - 109: 13.430 distance: 108 - 113: 12.056 distance: 110 - 111: 51.780 distance: 111 - 112: 19.267